delta nmr software user’s guide - berea college user’s guide, v 3.2 table of contents table of...

DELTA User’s Guide, v 3.2

Delta NMR SoftwareUser’s Guide

Copyright 1990-2000 by JEOL USA, INC.Eleven Dearborn Road

Peabody, MA 01960-3823All Rights Reserved


Trademarks• GLTM, Indigo®, Indigo MagicTM, Indigo2TM,IRIX®, OpenGL®, SGITM, Silicon

Graphics® Octane®, and Silicon Graphics® are trademarks of Silicon Graphics, Inc.• UNIX is a trademark registered in the United States and other countries, licensed

exclusively through X/Open Company, Ltd.• X Window System is a trademark of Massachusetts Institute of Technology.• Motif is a trademark of Open Software Foundation, Inc.• PostScript® is a trademark of Adobe Systems Incorporated• All other company and product names are trademarks or registered trademarks of their

respective companies.


Table of Contents

Table of Contents................................................................................................................. iList of Figures .................................................................................................................... ixList of Tables ................................................................................................................... xiii

Chapter 1. Introduction................................................................................................... 1-1Introduction................................................................................................................ 1-1About This Guide....................................................................................................... 1-1Before You Begin ...................................................................................................... 1-1Special Symbols......................................................................................................... 1-1Font Conventions ....................................................................................................... 1-1Keystroke Conventions.............................................................................................. 1-2Color Conventions ..................................................................................................... 1-2

Chapter 2. User Interface Basics .................................................................................... 2-1Power-on .................................................................................................................... 2-1Login .......................................................................................................................... 2-1Mouse and Keyboard ................................................................................................. 2-3

Input Focus........................................................................................................... 2-3Keyboard.............................................................................................................. 2-3Structure of a Window......................................................................................... 2-3

Window Menu Buttons .............................................................................................. 2-4“Iconifying” or Minimizing Windows....................................................................... 2-5Maximizing Windows to Full Screen ........................................................................ 2-6Moving Windows....................................................................................................... 2-6Resizing Windows ..................................................................................................... 2-6Toolchest.................................................................................................................... 2-6Workstation System Usage ........................................................................................ 2-8Terminal Shell............................................................................................................ 2-8Logout Window ......................................................................................................... 2-9

Chapter 3. Getting Started On Delta .............................................................................. 3-1Introduction................................................................................................................ 3-1Starting DELTA......................................................................................................... 3-1The Delta Console...................................................................................................... 3-2The Delta Console Menu Bar .................................................................................... 3-3

Pull-Down Menus ................................................................................................ 3-3Accelerator Keys.................................................................................................. 3-3

Tool Bar Icons............................................................................................................ 3-3Exiting Delta .............................................................................................................. 3-6On-line Help .............................................................................................................. 3-6Preferences Tool ........................................................................................................ 3-7File Manager ............................................................................................................ 3-15File Converter .......................................................................................................... 3-17

Chapter 4. Eclipse Spectrometer Control ....................................................................... 4-1


Introduction................................................................................................................ 4-1Spectrometer to Host Workstation Communication .................................................. 4-1Spectrometer Control Tool ........................................................................................ 4-2Selecting a Spectrometer............................................................................................ 4-2

Default Spectrometer Connection........................................................................ 4-5Spectrometer Control Tools....................................................................................... 4-7 Spectrometer Control Tools...................................................................................... 4-9Sample Control Tool.................................................................................................. 4-9

Shim Tool Controls............................................................................................ 4-13Queue Management ................................................................................................. 4-21

Experiment Data ................................................................................................ 4-22Additional Experiment Information................................................................... 4-23 Deleting Queue items........................................................................................ 4-23

Experiment Tool ...................................................................................................... 4-24 Experiment Selection ........................................................................................ 4-25Local Experiment Directory .............................................................................. 4-25Global Experiment Directory............................................................................. 4-25Loading an Experiment...................................................................................... 4-26The Header Section............................................................................................ 4-26The Instrument Section ...................................................................................... 4-29The Acquisition Section..................................................................................... 4-30The Pulse Section............................................................................................... 4-31

Automation Window................................................................................................ 4-34Automation Queue ............................................................................................. 4-37

Automation Console ................................................................................................ 4-38Automation Editor ................................................................................................... 4-39

Methods for Customizing Automation .............................................................. 4-41Lock Signal Display - Sawtooth .............................................................................. 4-43View Tool ................................................................................................................ 4-44Copy......................................................................................................................... 4-46

Chapter 5. Processing 1D Data....................................................................................... 5-1Introduction................................................................................................................ 5-11D Processor .............................................................................................................. 5-2

Default Start-up Mode ......................................................................................... 5-31D Processor Start-Up Procedure .............................................................................. 5-4

The Open File Tool.............................................................................................. 5-41D Processor Window - Extended Mode................................................................... 5-6

Processing Lists ................................................................................................... 5-7Extended Mode Icon Buttons - Top Row .......................................................... 5-10Extended Mode 1D Processing Icons -- Second Row ....................................... 5-13

Menus for Extended 1D Processing......................................................................... 5-14PreTransform Functions..................................................................................... 5-14Window Functions ............................................................................................. 5-17Transform Functions.......................................................................................... 5-17

Cursor Tool .............................................................................................................. 5-19Cursor Modes........................................................................................................... 5-22


Zoom, Region, PiP -- a Sampler ........................................................................ 5-23 Menus for Extended 1D Processing........................................................................ 5-26

Post Transform Functions .................................................................................. 5-26Display Functions .............................................................................................. 5-33Integrals.............................................................................................................. 5-46Peak Deconvolution ........................................................................................... 5-51Annotation.......................................................................................................... 5-55Molecules........................................................................................................... 5-57

Data Window Manipulations: Level Tool ............................................................... 5-59Data Window Manipulations: Geometry Options Menu......................................... 5-60Data Information Display: Spreadsheet Tool .......................................................... 5-64

Loading Data into the Spread Sheet................................................................... 5-65Drag and Drop.................................................................................................... 5-65

Saving Processed Data............................................................................................. 5-66Plotting Data ............................................................................................................ 5-67Presentation Manager............................................................................................... 5-69

Presentation Manager Templates....................................................................... 5-70Presentation Manager Boxes.............................................................................. 5-72Ruler Links Tool ................................................................................................ 5-72

Presentation Manager Menus................................................................................... 5-77Presentation Manager Tool Bar ............................................................................... 5-77Simple Mode 1D Processing.................................................................................... 5-78

Simple Mode Processor Buttons........................................................................ 5-79

Chapter 6. Using Data Slate ........................................................................................... 6-1Loading Data into the Data Slate ............................................................................... 6-2

Data Source Toggle Buttons ................................................................................ 6-2Loading Multiple Data Files ...................................................................................... 6-3

Horizontal and Vertical Views............................................................................. 6-3Box Data View..................................................................................................... 6-4

Selecting Active Data Sets......................................................................................... 6-5Data Slate Icons ......................................................................................................... 6-7

The File Math Tool ............................................................................................ 6-10Connected Objects ................................................................................................... 6-11

Individual Data Presentation Control................................................................. 6-12Panning, Rotating and Expanding Data ............................................................. 6-13

Peak Picking, Data Reduction and Integration ........................................................ 6-14Peak Deconvolution ........................................................................................... 6-14

Annotation................................................................................................................ 6-14Spreadsheet Tool...................................................................................................... 6-14Plotting Data ............................................................................................................ 6-14Connect Options on the View Menu........................................................................ 6-15Advanced Data Slate Operations ............................................................................. 6-15

Slicing ................................................................................................................ 6-15Expansion........................................................................................................... 6-17

Chapter 7. Processing 2D Data....................................................................................... 7-1


Introduction................................................................................................................ 7-1Loading 2D Data into the nD Processor .................................................................... 7-1Elements of 2D Processing ........................................................................................ 7-3Preparing 2D Processing Lists ................................................................................... 7-5

Selecting a Data Output destination..................................................................... 7-8Toggling between processing list view and geometry view: ............................... 7-9Selecting Preferences ........................................................................................... 7-9

Loading and Processing 1D Slices............................................................................. 7-9Phasing 2D Data ...................................................................................................... 7-10

2D Phasing Tool ................................................................................................ 7-102D Viewer Tool ....................................................................................................... 7-13

Two Dimensional Display Modes ..................................................................... 7-142D Cursor Tool functions .................................................................................. 7-17Contouring 2D Data........................................................................................... 7-17Overview Area ................................................................................................... 7-21Zooming and Panning 2D Data.......................................................................... 7-21Slice and Projection Areas ................................................................................. 7-22

2D Peak Pick and Data Reduction ........................................................................... 7-23Peak Grouping ................................................................................................... 7-25Peak Melding ..................................................................................................... 7-26Integrating 2D Data............................................................................................ 7-27Annotating 2D Spectra....................................................................................... 7-27Spreadsheet Tool................................................................................................ 7-30Plotting 2D Data ............................................................................................... 7-30

Chapter 8. Processing Relaxation Data .......................................................................... 8-1Introduction................................................................................................................ 8-1Collecting Relaxation Data ........................................................................................ 8-1Collecting T1 Data..................................................................................................... 8-3Calculating Relaxation Times.................................................................................... 8-3

Chapter 9. Processing 3D Data....................................................................................... 9-1Introduction................................................................................................................ 9-1Loading 3D Data into the nD Processor .................................................................... 9-1Elements of 3D Processing ........................................................................................ 9-2

Domains ............................................................................................................... 9-2Processing Lists ................................................................................................... 9-3Creating a Processing List ................................................................................... 9-5Building and Manipulating Processing Lists ....................................................... 9-6Editing a Processing List ..................................................................................... 9-6Loading and Processing 1D Slices....................................................................... 9-7

3D Data Slate ............................................................................................................. 9-83D Viewer.................................................................................................................. 9-8

Three-Dimensional Display Modes ................................................................... 9-10Loading 3D Data................................................................................................ 9-12

3D Slicer .................................................................................................................. 9-12Multidimensional geometry options .................................................................. 9-13


3D Slice Plotter ........................................................................................................ 9-13Cursor Tool ........................................................................................................ 9-15Rotating and Translating 3D Data ..................................................................... 9-18Slice and Projection Areas ................................................................................. 9-183D Peak Pick and Data Reduction ..................................................................... 9-18

Chapter 10. Experiment Tool and Eclipse Experiment Programming......................... 10-1Introduction.............................................................................................................. 10-1Definition ................................................................................................................. 10-1

Pulse Sequences ................................................................................................. 10-2Parameter Files................................................................................................... 10-2

Loading Experiments ............................................................................................... 10-2Spectrometer Control Tool ................................................................................ 10-2

Experiment Tool ...................................................................................................... 10-5Loading Experiments from Other Data Sets...................................................... 10-5

Syntax and Operators............................................................................................... 10-7Syntax Rules ...................................................................................................... 10-7Operators............................................................................................................ 10-8Define statement .............................................................................................. 10-13Strings .............................................................................................................. 10-13Units................................................................................................................. 10-14Align ................................................................................................................ 10-14Macro ............................................................................................................... 10-14Loop ................................................................................................................. 10-15Begin ................................................................................................................ 10-15Conditional if-then-else statements.................................................................. 10-15

Include files............................................................................................................ 10-16User Include Files ............................................................................................ 10-16Standard Include Files...................................................................................... 10-16Standard Include Files..................................................................................... 10-16

Header Section ....................................................................................................... 10-17filename............................................................................................................ 10-17sample_id ......................................................................................................... 10-18comment........................................................................................................... 10-18process.............................................................................................................. 10-18Autosample Changer slot................................................................................. 10-19Header Flags .................................................................................................... 10-19Header Parameters ........................................................................................... 10-22Adding Header Flags and Parameters Dynamically ........................................ 10-23

Instrument Section ................................................................................................. 10-23Solvent ............................................................................................................. 10-24Receiver gain (recvr_gain)............................................................................... 10-24Temperature control (temp_state and temp_set).............................................. 10-25Adding Instrument Parameters Dynamically................................................... 10-26

Acquisition Section................................................................................................ 10-26Domains ........................................................................................................... 10-27Spectral Offset ................................................................................................. 10-27


Spectral (Sweep) Widths.................................................................................. 10-28Data Points ....................................................................................................... 10-28Scans ................................................................................................................ 10-28Prescans............................................................................................................ 10-29

Pulse Section.......................................................................................................... 10-29total_time ......................................................................................................... 10-30x_pulse ............................................................................................................. 10-30 relaxation_delay.............................................................................................. 10-30j_constant ......................................................................................................... 10-30

Submitting Experiments ........................................................................................ 10-32Probe Codes and Probe Files ........................................................................... 10-32Probe Attributes ............................................................................................... 10-3390 Degree Pulses.............................................................................................. 10-33Spin Lock Pulses.............................................................................................. 10-34Temperature Limits.......................................................................................... 10-34Irr_code ............................................................................................................ 10-34Domains ........................................................................................................... 10-35Probe Tuning Values........................................................................................ 10-35

Calculations............................................................................................................ 10-36Calculation of Pulse Widths and Angles ......................................................... 10-36Calculation of Audio Filter Delays .................................................................. 10-37Total Time........................................................................................................ 10-38

Phase Tables........................................................................................................... 10-38Concatenation of Phase Sets ............................................................................ 10-39Addition of Phase Sets ..................................................................................... 10-3990 Degree Phases ............................................................................................. 10-40Sub-90 Degree Phases...................................................................................... 10-40

Multiple Buffer Acquisition................................................................................... 10-40module_config Options.......................................................................................... 10-41

Hardware Options ............................................................................................ 10-41Collection Mode..................................................................................................... 10-43Macros.................................................................................................................... 10-43Pulse Programs....................................................................................................... 10-44

Specifications................................................................................................... 10-44Begin/end Statement ........................................................................................ 10-44Time States....................................................................................................... 10-44Referencing Time Variables ............................................................................ 10-44Referencing Spectrometer Parameters............................................................. 10-44In-line Calculations.......................................................................................... 10-45End of Sequence .............................................................................................. 10-45

Gate Assignments and Options.............................................................................. 10-45RF Gates........................................................................................................... 10-46RF Phase .......................................................................................................... 10-46Attenuators....................................................................................................... 10-46Frequency Offset.............................................................................................. 10-46Noise Modulation............................................................................................. 10-46


Acquisition Macro ........................................................................................... 10-47Interactions with irr_code and module_config ................................................ 10-47

Compiling and Error Messages.............................................................................. 10-48Arrayed Parameters................................................................................................ 10-48

Interaction with multi_file Option ................................................................... 10-48Syntax .............................................................................................................. 10-49

Exceptions to Arrayed Parameters......................................................................... 10-50Setting Array Parameters ....................................................................................... 10-50Collecting T1 Data................................................................................................. 10-51

Appendix A. Standard Include Files A-1std_acquisition .......................................................................................................... A-1std_2d_acquisition .................................................................................................... A-1std_3d_acquisition .................................................................................................... A-2set_dec_instrument ................................................................................................... A-2std_domains .............................................................................................................. A-3std_domaind_master_list .......................................................................................... A-3std_header ................................................................................................................. A-4std_instrument........................................................................................................... A-5std_pulse ................................................................................................................... A-5std_solid_instrument ................................................................................................. A-6

Appendix B. Instrument Parameters B-1

Appendix C. Irradiation Codes C-1

Appendix D. Decoupling on a GX, GSX, or CPF Delta Upgrade Spectrometer D-1Proton decoupling from either IRR or TRR channel ................................................ D-1High Power 1H Decoupler Sequences from either IRR or TRR channel................. D-2Bilevel 1H Decoupling ............................................................................................. D-2Low frequency (X-nucleus) decoupling from the TRR channel .............................. D-2

Appendix E. Directories and Files used by Delta E-1Delta User Account....................................................................................................E-1Delta System Directories, /usr/delta/ .........................................................................E-3/usr/delta/global/ Files................................................................................................E-3/usr/delta/global/ Directories....................................................................................E-13/usr/delta/setup/ ........................................................................................................E-14Eclipse Files for Acquisition system........................................................................E-16Delta Configuration Files.........................................................................................E-17Eclipse Spectrometer Files and Directories .............................................................E-46Machine action files.................................................................................................E-59

/eclipse/shapes/ ..................................................................................................E-63/eclipse/ Program Files.......................................................................................E-64/usr/eclipse/testprogs/.........................................................................................E-67/etc/init.d ............................................................................................................E-68

Appendix F. Description of the Automation Template File F-1SAMPLES .................................................................................................................F-1METHODS ................................................................................................................F-2


GROUPS....................................................................................................................F-3EXPERIMENTS and PRESENTATIONS ................................................................F-4

Experiments .........................................................................................................F-4Presentations ........................................................................................................F-7

Logic of Flow in the Automation Editor....................................................................F-9

Appendix G. Presentation Manager and Template File Format G-1Console commands ................................................................................................... G-1

A sample template File (.pmt) ............................................................................ G-2

Appendix H. Terminal Console Program H-1

Appendix I. Tool Icons I-1

Appendix J. Unix and Vi Commands J-1I. Unix Commands ......................................................................................................J-1II. VI Commands ........................................................................................................J-2

Appendix K. Installing JEOL AutoTune probes K-1Probe Tuning............................................................................................................. K-3

Appendix L. Delta V3.2 Software Installation and Configuration Instructions L-1I. System Requirements for Delta V3.2 .....................................................................L-1

Workstations: .......................................................................................................L-1SGI - IRIX: .........................................................................................................L-1Intel - Linux .........................................................................................................L-1IBM - AIX............................................................................................................L-2Sun - Solaris.........................................................................................................L-2Acquisition Systems: ...........................................................................................L-2NMR Spectrometers: ...........................................................................................L-2

II. Preparing for the Delta V3.2 Software Installation or Upgrade............................L-2III. Installing or Upgrading the Delta Software on SGI IRIX Systems ..................L-3IV. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from anSGI Workstation ........................................................................................................L-5V. Installing or Upgrading the Delta Software on Intel Linux or Sun Solaris Systems ..L-6VI. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System fromLinux, or Solaris.........................................................................................................L-7VII. Installing or Upgrading the Delta Software on IBM AIX Systems ...................L-7VIII. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System fromAIX. ...........................................................................................................................L-8IX. USER Account Setup ..........................................................................................L-8

Appendix M. X Windows Emulation M-1SGI IRIX setup: ..................................................................................................M-1X-Server Requirements for PC or MAC:............................................................M-1PC X-Servers: .....................................................................................................M-2MAC X-Servers: .................................................................................................M-2

Index ..................................................................................................................................I-i

DELTA User’s Guide, v 3.2 ix

List of Figures

Silicon Graphics Login Screen 2-1Silicon Graphics User Interface Screen (detail) 2-2Basic IRIX Window Structure 2-4Window Menu Button 2-5Minimized and Maximized Windows 2-5Moving and Resizing Windows 2-6Silicon Graphics User Toolchest 2-7“Selected” Menu 2-7System Usage Monitor 2-8Silicon Graphics UNIX Shell Window 2-9Silicon Graphics Logout Confirmation Window 2-9The Delta Console Window 3-2Delta Console Menu Bar 3-3Delta Console Tool Bar 3-4Confirm window 3-6Preferences Tool - Personal Page 3-7Search Tool 3-10Directory Tool 3-11Preferences Tool - Data Page 3-12Preferences Tool - Geometry Page 3-13Preferences Tool - Miscellaneous Page 3-14File Manager 3-15Data File Converter 3-17Delta Console Window 4-2Spectrometer Control Tool 4-3Spectrometer Control Tool Top Buttons 4-3Spectrometer Control Tool Info Display 4-4Spectrometer Control window after connection of the workstation and spectrometer 4-5Spectrometer Control Tool in Monitor Mode 4-6Spectrometer Control Tool Lower Buttons 4-7Sample/Shim Tool 4-9Lock Control section displays the NMR-lock level 4-13Set the axis for shimming 4-13System Shims Acknowledge Window 4-15Open Shim File window 4-16Save Shim File window 4-17Lock Level Meter (Minimum 0, Maximum 4095) 4-18Lock Control 4-18Gradient Shim and Lock Buttons 4-18Acknowledge message window 4-22Spectrometer Control with Experiment Pending 4-22Spectrometer Control with Experiment Running 4-22Experiment Information Window 4-23

x DELTA User’s Guide, v 3.2

Open Experiment Tool 4-25Experiment Header Section 4-27Set Process Window 4-28Experiment Instrument Section 4-30Experiment Acquisition Section 4-31Experiment Pulse Section 4-32Pulse Viewer 4-33Automation Tool 4-34Automation Queue Window 4-37Automation Console 4-38Automation Editor 4-39Flow Chart for an Automation Editor 4-42SAWTH or swept lock signal display 4-44View Tool -- raw data 4-45View Tool - processed data 4-461D Processor 5-11D Processor with untransformed and processed data 5-2Open File Tool Window 5-4Extended Mode 1D Processor after Performing FFT and Phasing 5-61D Processing List 5-7Open Process List window 5-8Save Data File window 5-12Empty Process List 5-16Process List after Adding DC balance 5-16Process List after Adding DC Balance and Zerofilling 5-16Process list after adding Window function 5-17Process list after adding Fast Fourier Transform 5-181D Zoom mode operations 5-19Sample Key command menu 5-21Sample Zoom Operation 5-23Sample Region Operation 5-24Sample PiP Operation 5-25Spectrum before Phase Correction. 5-27Phase Correction Performed Using P0 5-28Further Phase Correction Using P1 5-28Applying the Phase Correction 5-29Interactive Baseline Correction - a) Polynomial and b) Piece wise Linear 5-31Interactive Baseline Correction Preview 5-32Interactive Baseline Correction with Show Curve Enabled 5-32Process list after converting data axis to PPM 5-34Reference Tool 5-34Reference in Processing List 5-35Copy Reference Tool 5-36Spreadsheet Tool 5-381D Processor with auto-peakpicked 1H data 5-401D Processor with adjusted peak threshold 5-41

DELTA User’s Guide, v 3.2 xi

Pick Tool 5-42Peak Pick Threshold Display 5-43Peak Display (default) 5-45Peak Display with Peaks Above Option Enabled 5-46Peak Display with J Coupling Constants 5-461D processor with data peaks integrated 5-47Integral Slope Adjustment 5-49Transfer Integral Tool 5-51Data before Deconvolution 5-52Deconvolved Data 5-52Deconvolved Data with Deconvolve Sum 5-54Deconvolved Data with Deconvolve Unsel 5-54Spreadsheet after a Deconvolution 5-55Annotation Rotation & Shift Keys 5-56Data after Annotation 5-57Level Tool -- Contour View (I) and Colors View (II) 5-59Zoomed view of data showing Data points 5-61Spreadsheet Tool 5-65Save Data File Window 5-67Print Options Window 5-68Presentation Manager 5-69Ruler Links (Links) 5-73Ruler Limits 5-74Ruler Links (Y Scale) 5-75Presentation Manager (Preview) 5-76Simple Mode 1D Processor 5-78Data Slate 6-1Vertical Data Slate Views 6-3Horizontal Data Slate Views 6-4Box Data Slate View 6-4Data Overlay 6-6Print Options 6-8Resulting File Window 6-11Connection Tool after and before a Connection is Made 6-12Geometry Tool 6-13Data Slate Slicing Menu 6-16Data Slate Slicing 6-16Expand Options Menu 6-17Data Slate Expand Display 6-18Expand Size Selection 6-18Open File 7-2Empty nD Processor 7-3nD Processor Window 7-4X-Domain processing list 7-5nD Process Data Destination Buttons 7-82D Phasing Tool 7-11

xii DELTA User’s Guide, v 3.2

2D Phasing Tool Region Display 7-122D Viewer - Contour Mode 7-13Mesh(a), Surface(b), Stack(c), and Image(d) Modes 7-16Level Tool 7-18Data with too few (only topmost) contours selected 7-20Data with too many contours selected (well into the noise floor) 7-20Data with a sensible distribution of contours selected 7-21Peak Pick Overlay 7-232D Peak Pick Display 7-242D Peak Multiplet with Fine Structure 7-25Peak Grouping 7-26Peak Melding 7-262D Integration. 7-272D Annotation 7-282D Spreadsheet 7-30T1 Analyze Tool 8-4Open Data for Processing Window 9-2Empty 3D Processor Window 9-33D Data Slate 9-83D Viewer Right Mouse Button Mode Selection Menus 9-93D Viewer 9-103D Viewer - Slices 9-113D Viewer - Zoomed 9-113D Slicer with Overlaid Spears 9-123D View Control 9-17Spectrometer Control Tool after Connection 10-3Open Experiment File Tool 10-4Experiment Tool 10-5Experiment Tool Header 10-17Adding Header Fields 10-23Experiment Tool Instrument Section 10-24Adding Instrument Parameters 10-26Experiment Tool Acquisition Section 10-27Experiment Tool Pulse Section 10-30Pulse Display Widget 10-31Set Array Parameters Windows 10-51


List of Tables

Window Menu Functions2-4Delta Console Tool Bar Icons3-4Shim Tool Nomenclature 4-14Data Slate Icons6-7Connect Functions6-15Relaxation Experiment8-2Experiment Tool Icons10-5Experiment Header Parameter Definitions10-10Experiment Acquisition Parameter Definitions10-12Experiment Pulse Parameter Definitions10-13Header Process Information Options10-18Header Flags10-19Temperature Parameter List10-25Scans Parameter Limits10-29Eclipse Probe Code List10-33GX, GSX and CPF Assignments 10-33IRR Codes for Probes10-34Multiple Buffer Phase Cycles10-41RF Channel settings10-41Time-shared Homonuclear Decoupling10-42Noise Modulation Gating10-42Amplifier Power Settings10-42Combination Features10-42PGX-300 Pulser Specifications10-44Irradiation Modulation Modes10-47Irradiation CodesC-1Conversion Example for TH5 ProbeC-1GX Decoupler Amplifier ControlD-1Delta NMR software package componentsL-4

DELTA User’s Guide, v 3.2 1-1

CHAPTER 1: INTRODUCTION

INTRODUCTION

DELTA is a graphically-oriented NMR data processing software package running onSilicon Graphics computer workstations. DELTA uses a mouse-driven graphical userinterface with pull-down menus and icons to perform common NMR data manipulationsand to control the Eclipse NMR spectrometer.

ABOUT THIS GUIDE

This DELTA NMR Software User's Guide provides a useful overview of DELTA. Itcovers basic 1D, 2D, and nD NMR processing and data acquisition (see Chapters 5 and 7).For more information about the Eclipse NMR spectrometer, please consult Chapter 4.Other chapters and appendices provide a wealth of information. The introduction to eachchapter provides links to its important topics. For further information on specific featuresof the DELTA software, consult the Delta User’s Reference and Online Help, or thePercival Reference Manual.

BEFORE YOU BEGIN

DELTA must be correctly installed and configured on your workstation or network. If theDELTA software does not run correctly, please consult your system manager. Refer toAppendix L, “Delta V3.2 Software Installation and Configuration Instructions”.

You must have an account on the workstation that runs the software. Please see yoursystem manager to set up an account for you.

SPECIAL SYMBOLS

Special attention:This symbol marks an important explanation of an operation or a function.

Warning:This symbol indicates that the operation could seriously affect operation of thesoftware or hardware.

FONT CONVENTIONS

File names which are part of the DELTA software are shown in Courier font (forexample,.delta_configure). Courier font is also used to designate UNIXconsole input, sample file contents, and output from DELTA programsin a console window.

DELTA commands and tools are shown in bold type.

Chapter 1: Introduction

1-2 DELTA User’s Guide, v 3.2

References to other manual names are shown in Times bold italics.

SGI commands and window titles are shown in Helvetica bold italics.

KEYSTROKE CONVENTIONS

Two modifier keys are commonly used as “accelerator keys” or as keyboard shortcuts:

• The CONTROL key is abbreviated in this manual as CTRL, or represented with the“^” character used in all the DELTA menus. For example, CTRL-G or ^G meanspress the CONTROL key, then press the “g” key.

Note that DELTA “accelerator keys” are never case sensitive, whereas UNIXcommands are always case sensitive.

CTRL-1 means hold down the CTRL key, and then press the number “1” key. Zero(0) is also spelled out (CTRL-zero) to avoid confusion with the letter O.

• The ALTERNATE key is abbreviated ALT in this manual. ATL-g means hold downthe ALT key, then press the “g” key.

Note that, in SGI Windows Menus, ALT+F1 means hold down theALTERNATE key, then press the F1 key.

• The ESCAPE key is abbreviated in this manual as ESC.

• The SPACEBAR key is abbreviated in this manual as SPACE.

COLOR CONVENTIONS

When a color is mentioned, it is assumed that the DELTA software is running with thedefault color scheme. If you customize the color scheme with the Configuration Editor orby editing the.delta_configure file, the colors mentioned in the manual may notmatch your screen display.

It is not advisable to change different color preferences to the same color.Doing so may cause parts of the display to be obscured by other parts whosecolor is the same. Displaying data using the same color as the backgroundcolor is definitely not advised!


CHAPTER 2: USER INTERFACE BASICS

This chapter covers only the basic operation of the Silicon Graphics user interface as itpertains to DELTA. For additional information, consult the documentation that came withyour workstation. Some window features may not be available or active in other softwareapplications.

POWER-ON

Consult the Silicon Graphics documentation that came with your workstation to determinethe location of the power switches for both computer and monitor. Before proceeding,make sure that the workstation and monitor are turned on.

LOGIN

Please refer to Figure 2-1.

Figure 2-1. Silicon Graphics Login Screen

❏ To log onto the workstation:• Double-click on the DELTA icon with your mouse:

• A password box will appear on the screen.

DELTA-J

Chapter 2: User Interface Basics


• Place the mouse in this box and type your password. If the password is correct, thiswindow will open (see Figure 2-2).

The following figures and pictures may look different on your screen if you arerunning a different version of the UNIX operating system on your workstation.

Figure 2-2. Silicon Graphics User Interface Screen (detail)

Silicon Graphics provides you with a graphical user interface (GUI) in which you initiateand input instructions using the mouse and cursor position. This contrasts with the olderstyle command line (text) user interface where all commands are entered by typing on akeyboard. The keyboard is still used for text input, but the location is selected by themouse cursor.

Another important characteristic of the Silicon Graphics user interface is that multiplewindows display on the screen simultaneously. Each window may represent a separateprogram, or a different part of a single application. Windows may perform operationssimultaneously. Windows may be “iconified” to recover screen space or to move awindow out of the way.

DELTA-J

delta Delta UserPassword: password input box

Mouse and Keyboard


MOUSE AND KEYBOARD

All user input is made using the keyboard and the mouse. The mouse controls a pointer orcursor on the screen. The shape of the mouse cursor will change, depending on the mode.The mouse has three buttons: left, middle, and right. The left mouse button is the mostcommonly used button for selecting objects, although all three buttons are used in DELTA.

Input FocusBecause multiple windows can be displayed simultaneously on the screen, the user mustunderstand the concept of “input focus.” The “input focus,” or “active window,” isdetermined by the position of the mouse cursor on the screen. To enter text or otherkeyboard input, the mouse cursor must be in the desired window and at the desiredlocation in the window. As the mouse moves from one window to another, the windowborder and window title bar will change from a dark to a lighter gray color to mark theactive input focus window.

❏ To click the mouse:Press down briefly, then release the mouse button. The mouse button to use -- left, middle,or right -- may be specified. Use the left mouse button unless this manual specifies themiddle or right mouse button. A mouse click is also called a “single click.”

Certain operations may be performed by a “double click” -- two single clicks in rapidsuccession. The second click of a double click sequence is interpreted as an “OK.” For thisreason, double clicks are commonly used to select files.

Do not develop a habit of excessively clicking the mouse. The response time ofthe workstation may slow during times of high CPU loading. However, theDelta software will remember all the mouse clicks and all of them will beexecuted as time allows. Unwanted functions could be performed!

❏ To drag the mouse:Press the mouse button and hold it down while moving the mouse to a new location.Dragging the mouse is commonly used for repositioning and resizing windows on thescreen.

KeyboardUse the keyboard for all text input. The keypad may also be used for numeric input. Arrowkeys may also be used for zooming and panning the NMR data. The keyboard functionkeys (F1 through F12) are also assigned to special functions inside the Delta software.

Structure of a WindowThe basic structure of a window is shown in Figure 2-3. This figure shows the mostcommonly used parts of a window. For more detailed information, see “Anatomy of aWindow” in the section “Getting Started” shown in the Index for Desktop Help. This can beviewed by selecting Desktop Help from the Help submenu in the standard Toolchest. (Seethe Toolchest section on page 2-6.)



Figure 2-3. Basic IRIX Window Structure

WINDOW MENU BUTTONS

On the left top corner of the window is a menu button, shown in Figure 2-4. Click with themouse to display a menu of window options. The menu will remain displayed after themouse button is released. Click with the right mouse button in the Title bar to display thesame menu of window options; this menu will disappear when the mouse button isreleased. Drag the mouse to the desired option, then release, to execute the selectedfunction. The most useful functions are Raise, Lower, and Quit.

Table 2-1: Window Menu Functions

Select:

Restore Alt F5 To refresh the Delta Console window.

Move Alt F7 To move the Delta Console window.

Size Alt F8 To change the window size.

Minimize Alt F9 To turn the window into a postage stamp size icon.

Maximize Alt F10 To size the window to fill the terminal screen.

Raise Alt F1 To position the window in front of the other windows.

Lower Alt F3 To position the window in back of the other windows.

Close To close the window.

Path Bar

Pathname

Drop Pocket

FieldRecycleButton

Maximize ButtonWindow TitleWindow Menu Button

Scroll BarsWindow Border

Iconize Button

“Iconifying” or Minimizing Windows


Note: If there is a key combination next to the function, the keyboardcombination will effect the same operation. These keyboard combinations arecalled “accelerator keys.”

Figure 2-4. Window Menu Button

“ICONIFYING” OR MINIMIZING WINDOWS

Figure 2-5 shows two symbols that appear on the right side of the window menu bar. Clickon the small square icon to minimize (or iconify) the window. Click again on the smalliconified window to restore it to the original size.

Figure 2-5. Minimized and Maximized Windows

mouse click

Minimize (Alt+F8) Maximize (Alt+F10)[or Restore (Alt+F5)][or Iconifying]



MAXIMIZING WINDOWS TO FULL SCREEN

Clicking on the large square shown in Figure 2-5 causes the window to fill the entirescreen. The full screen window will cover all other windows. This button acts as a toggleswitch. Click on the large square again to restore the window to the original size.

MOVING WINDOWS

The title bar of a window displays the name of the window. If you position the mouse onthe title bar and drag the mouse while pressing the left button, you can move the window(visible as a red outline) to a new location. When the mouse button is released, thecontents of the window will be redrawn.

RESIZING WINDOWS

Windows displayed on the screen may be resized by selecting the border with the mouseand dragging it to a new position (see Figure 2-6.) The border and corners of a window arecalled “handles.” If you put the mouse pointer on the border or corner of a window, thepointer will change. This means you have “grabbed” the handle, and may resize thewindow by dragging the mouse from this point.

Figure 2-6. Moving and Resizing Windows

TOOLCHEST

A list of programs and utilities is displayed in the upper left corner of the screen asillustrated in Figure 2-7. This menu is called the “Toolchest.” If you select a category,programs within that category will appear. Drag the mouse to select the desired programor utility. The contents of the Toolchest are controlled by the.auxchestrc or.chestrc file in the user's home directory. The default Toolchest setup file is /usr/

Toolchest


lib/X11/system.chestrc. You should customize your own account by using the.auxchestrc file in the user's home directory. See “Modifying the Toolchest” in thesection “Customizing Your Environment” shown in the Index for Desktop Help. This can beviewed by selecting Desktop Help from the Help submenu in the standard Toolchest.

If the right mouse button is clicked on the screen background (any blank area of screenoutside a window), a menu is displayed as illustrated in Figure 2-8. If the workstation hasbeen configured by JEOL, the menu will allow you to open a UNIX terminal shell and tolog out; other options may also be available.

Figure 2-7. Silicon Graphics User Toolchest

Figure 2-8. “Selected” Menu



WORKSTATION SYSTEM USAGE

Each workstation has a utility program called gr_osview. This program, a performancemonitor for the system, is shown in Figure 2-9.• To start the monitor: select “System Usage” under the “Programs” option in the

Toolchest.• To close the monitor window: place the mouse in the window and press the ESC key.• To move this borderless window to another position on the screen: place the mouse

cursor over the gr_osview window and, while holding down the ALT key, hit theF7 key (ALT+F7). The cursor will change to a four-sided arrow. The red outline maynow be positioned anywhere on the screen. A mouse click will place the window at thenew position.

• To get the Window Menu (see Figure 2-4) for a borderless window: press the ALTkey and click the right mouse button. Unlike other borderless utility windows, thegr_osview window can not be resized.

For more information on the system monitor and gr_osview, consult the SGIdocumentation or the man pages for gr_osview.

Figure 2-9. System Usage Monitor

TERMINAL SHELL

A window containing a standard UNIX shell, as shown in Figure 2-10, can be created byusing the Desktop - Shell command located under the Toolchest menu. The Shell may belisted as Unix Shell, or Shell (terminal), depending on the operating system version.

Logout Window


Figure 2-10. Silicon Graphics UNIX Shell Window

LOGOUT WINDOW

To log out from the workstation: select Log Out from either the Background menu orthe Toolchest menu.

A logout will ask for a confirmation shown in Figure 2-11. Select Yes to log out. Allapplications and windows will be closed on logout.

Figure 2-11. Silicon Graphics Logout Confirmation Window


CHAPTER 3: GETTING STARTED ON DELTA

INTRODUCTION

This section will briefly describe the fundamental operation of basic DELTA processingtools. It covers procedures for:• starting Delta (page 3-1)• running Delta from the Delta Console menus and icons (page 3-3)• tailoring the look and feel of Delta using the Preferences Tool (page 3-7)• managing files (page 3-15)• converting files (page 3-17).

The DELTA software program is composed of tools. Each DELTA tool uses one or morewindows to process, analyze and/or plot NMR data. Each tool is built with “widgets”which offer you different ways of entering information or manipulating data on the screen.These widgets allow you to input parameters, select functions, execute processing, etc.

STARTING DELTA

After you have logged onto the workstation, do the following:1. Start the application by selecting “Delta” under Programs in the Toolchest menu in the

upper left-hand corner of the screen. Or Double-Click on the Delta icon in the GUIwindow.

Note: If DELTA is not listed under the Toolchest, see your system manager orconsult Appendix O, Section II.If DELTA is running over a network, start-up could be delayed slightly bynetwork traffic. If the application does not start up, look under the UNIX“Console” window for error messages, or use the “System Usage” tool tomonitor CPU performance.

Note: When running DELTA from your desktop, if autoplacement is turned onin the Miscellaneous Page of the Preferences Tool, then the DeltaConsole window will open automatically.

Note: Train yourself from the outset to give Delta clear signals. Delta respondsto each click of the mouse. For instance, use a single click of the mouse toopen a window (otherwise, Delta will read each signal and duplicate windowswill come up).

Double-click on the Delta icon

Chapter 3: Getting Started On Delta


Note: As a general rule, it is better to complete processing and analysis of thedata before employing virtual geometry features.

Note: Extremely large data files can slow down Delta.

THE DELTA CONSOLE

When you launch DELTA -- in all cases except where a preserve location is specified inthe.delta_configure file -- a red outline of the Delta Console (Figure 3-1)appears.

❏ To activate the window:Move the mouse to position the Delta Console window anywhere on the screen and clickto open the window. The window can be repositioned at any time.

The Delta Console window pull-down menus and icons are used to invoke all Delta tools.

❏ To activate either menus or icons:Place the mouse cursor on your selection and click.

This section will not cover all of the Delta Console options. For a moredetailed discussion, refer to the (See Delta User’s Reference: “The DeltaConsole” on page 6-1).

Figure 3-1. The Delta Console Window

The Delta Console Menu Bar


THE DELTA CONSOLE MENU BAR

Along the top of the Delta Console window frame is a selection of topics called theMenu Bar (Figure 3-2). The Menu Bar lets you use the mouse to select functions and toolsusing the mouse.

Figure 3-2. Delta Console Menu BarNote: The “User” menu is for user-defined choices. It is described in AppendixE on page 41.

Pull-Down Menus

Each topic on the Menu Bar has a pull-down menu like the one illustrated above. Clickand hold the mouse on a Menu Bar topic to display its menu of choices. Consult the Helpand Delta User’s Reference Guide for a description of these menus (page 6-4).

❏ To select an item from a pulldown menu:Drag the mouse down the list (keeping the mouse button pressed down) to highlight thedesired feature. If you have chosen an incorrect menu, simply move the mouse outside themenu and release the button.

Accelerator KeysAlso displayed in the pull-down menus are “accelerator key” combinations. Hit a keycombination on the keyboard to invoke a tool or an option. The carat character (^) on anaccelerator key in the pull-down menu indicates the CTRL key. For example, in themenu illustrated above, ^S means hit CTRL S to access the Presentation Manager.

TOOL BAR ICONS

Located below the Delta Console Menu Bar is a set of icons representing many commonlyused functions. This area is called the “Tool Bar” (Figure 3-3). Each icon has a uniquepicture that represents the tool or function you may select by clicking the mouse button.Clicking on the icon changes its appearance to that of a button that has been pressed down.Many of the Icon functions duplicate the functions under the Menu Bar. Table 3-1 listsand describes the function of these icons.



Note: Selecting any icon with the right mouse button will bring up a labelidentifying it.

Figure 3-3. Delta Console Tool Bar

Table 3-1: Delta Console Tool Bar Icons

Select:

To open the NMR data into a Data Processor. Thedimensional size of the data is checked and the correctprocessor invoked. See Chapter 5 for more information onusing the Data Processor (page 5-1).

Note: to start the 1D processor, you may eitherselect this Icon or select the 1D Processoroption under the Processors menu.

To use the Data Slate to display and manipulate 1D, 2D,and 3D data. See Chapter 6 for more information on usingthe Data Slate (page 6-1).

To use a Data Viewer to view NMR data. The window issized to the dimensions of the data displayed. See Chapter7 for more information on the 2D Data Viewer (page 7-13).

To navigate the subdirectories Delta uses for different files.The File Manager also allows you to copy, edit, delete,and rename files. Open this tool to consult its online Help.

To use the Presentation Manager to customize designof a printout of NMR data and to organize the differentprocessing of one or more data sets. Open this tool toconsult its online Help.

Tool Bar Icons


To display parameters and the processing history for anydata set. Open this tool to consult its online Help.

To use a Spreadsheet to display peak, integral andassignment information in table form. Open this tool toconsult its online Help (page 57-1).

To use the Connection Tool to create connectionsbetween different data sets. Use the axial reference scale toestablish links. Any data sets, regardless of data pointdensity, sweep width and field strength, may be connected.Open this tool to consult its online Help (page 19-1).

To use the Eclipse Spectrometer Connection utility toconnect to, or monitor, a spectrometer. See Chapter 4(page 4-1).

To use on-line help. Help will display a picture of the toolwith a brief description of its functionality.

To use the mouse cursor to finger text to cut from theselected data geometry into another window on the Deltaconsole.

Note: To clear an input box, double click theright mouse button.

To finger and paste text from the selected data geometry onthe Delta console to a preselected window. A Paste canalso be performed by clicking the middle mouse buttonwhen the cursor is in an input box.

Table 3-1: Delta Console Tool Bar Icons

Select:



EXITING DELTA

❏ To exit Delta after completing measurement or NMR data processing:

1. Select Quit in the File menu.

2. The Confirm window opens, asking whether you want to quit the program.

Figure 3-4. Confirm window

3. Select OK.

Note: If you decide not to quit the Delta program, click on the Cancel button.

ON-LINE HELP

Located on most tools in Delta is a help icon button, which connects you, via NetscapeBrowser, to a .MIF help file offering useful guidance on that tool. The contents of this helpfile are identical to the framemaker/.pdf version of the Delta User’s Reference Guide.

1. To start on-line help for the tool currently displaying on Delta: simply click on thehelp icon, or select Help in the menu bar.

2. Use the scroll bar to scroll up and down in the file.

Preferences Tool


PREFERENCES TOOL

Figure 3-5. Preferences Tool - Personal PageThe Delta Preferences Tool allows you to change the parameters that control the lookand feel of Delta. These parameters are kept in the .delta_configure file, whichresides in the user’s home directory and is described in Appendix E.

Note: The .delta_configure file is not meant to be edited with the texteditor, but with the Preferences Tool.Note: Most parameters take effect when they are changed, without restartingDelta. Every parameter listed in the Preferences Tool with a * next to itsname is one that does NOT take effect until Delta restarts.



❏ To invoke the Preferences Tool:Select File, then select Preferences, from the Delta Console window menu bar. Ascreen containing personal information about the user will display. At the top of thisscreen are icons that enable you to go from one page to any other page (or if you prefer,you can use the Options menu to access one of these pages or to configure the printer.)

❏ Use the icons to select a page in the Preferences Tool:

Select:

To return to the Personal Information Page illustratedabove from any other page.

To turn to the Directory Page, which contains a list ofavailable directories.

To select Printer and printer options such as orientation(landscape or portrait), paper size, tessellates, andparameter location.

To turn to the Data Page, which contains information andfeatures specific to the data found in geometries.

To turn to the Geometry Page, which containsinformation and features specific to the display of thegeometry.

To change the Alternate Cursor selections.

To select colors for displays, widgets, etc. You may alsoelect to display icons in black and white and changecolor mapping defaults.

Preferences Tool


❏ Use the buttons at the bottom of any pages to save new parameters or restore apage to its original settings:Selecting:

Saves modified preferences to .delta_configure and exits.

Restores only the parameters on the current page to their originalsettings.

Restores all parameters to their original settings.

To turn to the System page.

To turn to the Miscellaneous page.

To turn to the Delta Tools page.

To turn to the Processors page.

To turn to the Automation page.

Select:



Disregards the changes and exits the Preferences Tool.

Note: Click on any title on any page with the right mouse button to get a helplabel.

❏ To search in the preference settings and pop-up help for any keyword:

• Select Search in the Options menu. A search window pops up.• Type the word you want to find into the box marked Search: (geom was typed into

the Search Tool window illustrated below) Select the Go button.• The Search tool then returns a list of all preferences or popup help containing the

keyword (see the example below): page, # of preference on that page, title and whenthe word appears in the online help, that line of help.

• Select the reference you desire -- Colors #5, below - and click on it to go directly to it.

Figure 3-6. Search Tool

❏ To change parameters in the Preferences Tool:

Select a field with your mouse, and:• Type in a new value.• Select a new value from a list that appears.• Move the slider to increase/decrease a value.• Toggle the ON/OFF button.

❏ To start the directory tool:

Select . The Show Hidden Files button expands the directory tool to include filenames. You can either select a file from the File list or type in a filename. Select Apply toset the preference to the current directory. You can also drag the directory to a destinationby selecting the input box at the bottom of this tool.

Preferences Tool


Figure 3-7. Directory Tool

Sample pages from the Preferences Tool -- geometry page, data page, and misc page --follow. All pages of the Preferences Tool are discussed in detail in the online Help, SeeDelta User’s Reference: “Preferences Tool” on page 45-1.



Figure 3-8. Preferences Tool - Data Page

Preferences Tool


Figure 3-9. Preferences Tool - Geometry Page



Figure 3-10. Preferences Tool - Miscellaneous Page

File Manager


FILE MANAGER

Delta’s File Manager makes it possible to edit, compile, delete, move, copy, purge,inherit, or keep a processing history of files.

Figure 3-11. File Manager

❏ To invoke the File Manager:

• Select on the Delta Console.• Or, select the File Manager command from File Access in the File menu of Delta

Console.

❏ Select a file using the list and input boxes.The Directory Input Box displays the current directory.If you want to see a different directory, you can type the name of the directory andthe path to it in the input box, and then press the enter key.Subdirectory List Box lists all the subdirectories in the current directory.

File Toggle Buttons

Version Number List Box

File Management Buttons

DirectoryInput Box

SubdirectoryList

File ListBox

Tool Bar

Hop ButtonsDirectory

BoxFile Input

File Info



Note: if the Show Hidden Files option in the Options menu is toggled on, allthe hidden directories will be listed as well.

File List Box lists all files that are in the current directory.

Version Number List Box displays all version numbers of the selected file.

❏ Use the Tool bar icons to call up these tools with the selected file in them: (in order) Data Processor, Spectrum Phaser, Data Slate and Data Viewer:

An appropriate tool will be opened based on the dimension of the selected file.

Note: click and hold the right mouse button on the icon to reveal the name ofthe tool.

❏ Use the buttons along the right hand side to perform File Management Tooloperations.See Delta User’s Reference: “File Manager” on page 27-1 for a description of this tool.

File Converter


FILE CONVERTER

Figure 3-12. Data File Converter

Delta’s Data File Converter lets you copy a file from one format to another. See DeltaUser’s Reference: “File Converter” on page 26-1.

❏ To invoke the Data File Converter:Select File Conversion in the File menu of the Delta Console.



❏ To convert data:1. Select a file type button in the From column, then one in the To column to convert

from the first file type to the second selected.2. A blue arrow points from the source file to the output file.

Select:

To choose the directory and name of the file you want to convert. Youmay also enter the name of a Percival data file directly into the input box.

To choose the directory and filename to store converted data. You mayalso enter the name of the Percival data file directly into the output box.

To start converting the data.

To save the intermediate JEOL Generic files.

To exit the Conversion tool.

❏ Use the Options Menu:To toggle on/off automatic extension correction and the display of progress messages.


CHAPTER 4: ECLIPSE SPECTROMETER CONTROL

INTRODUCTION

DELTA communicates with and controls the Eclipse NMR spectrometer through severalseparate windows and tools. This section provides an introduction to these tools, andexamples of basic NMR spectrometer control. This chapter discusses the following toolsand processes:

• Spectrometer Control, page 4-2• Sample loading, page 4-9• Experiment and Queue management, page 4-21• Experiment, page 4-24• Experiment Automation, page 4-34• Automation Queue, page 4-37• Automation Editor, page 4-39• Sawth (Lock signal display), page 4-43, and• View Tool (Real-Time monitor display), page 4-44.

Note: To close any window: use the pull-down menu in the upper left corneror press the ESC key while that tool is the input focus.

SPECTROMETER TO HOST WORKSTATION COMMUNICATION

All communication from the workstation to the Eclipse spectrometer uses Ethernet usingthe TCP/IP Protocol. This means the user may establish and control an Eclipse NMRspectrometer thousands of miles away from the workstation. This distributed network hasmany benefits for multi-user environments.• Several different users from separate workstations can connect to the spectrometer to

submit experiments or to retrieve data.• Remote connection can even be established through a terminal emulator, or through X

window emulation.The Eclipse NMR spectrometer has a complete UNIX computer embedded inside it. Thatcomputer is assigned a TCP/IP node address and name. This node name is what displayswhen the Spectrometer Control Tool is started.

Chapter 4: Eclipse Spectrometer Control


SPECTROMETER CONTROL TOOL

❏ To invoke the Spectrometer Control Tool:

1. Click on this icon in the Delta Console window .

Figure 4.0-1. Delta Console Windowor select Acquisition, then Connect, from the Delta Console Menu Bar.

The Spectrometer Control Tool, from which all spectrometer functions and controlsmay be accessed, opens.

SELECTING A SPECTROMETER

When you start the Spectrometer Control Tool, its display screen lists all availableEclipse NMR spectrometers on the network (see below). If you have a single Eclipsespectrometer, only one node name is displayed

Selecting a Spectrometer


.

Figure 4-1. Spectrometer Control Tool

❏ Use these Spectrometer Control Tool function buttons (Figure 4-2):

• Info to get information about a particular spectrometer (page 4-3),• Connect to connect (page 4-4) or Monitor to monitor a spectrometer (page 4-6),• Unlink (page 4-7) to terminate connection to a spectrometer, or• Free (page 4-7) to “ping” the network for the status of the spectrometers.

Figure 4-2. Spectrometer Control Tool Top ButtonsSelect:

to display the contents of the machine.info file from the currently selectedspectrometer (Figure 4-3).



Figure 4-3. Spectrometer Control Tool Info Display

Select:

after first selecting a spectrometer, to connect to a FREE spectrometer, and to gainownership of the spectrometer and control of all its features. Depending on Ethernettraffic, it may take several seconds to establish connection. During this time, theworkstation is uploading parameters from the spectrometer.

The spectrometer name will be displayed in reverse video. If connection is successful, themessage Connect is displayed at the top of the window, as shown in Figure 4-4.

Selecting a Spectrometer


Figure 4-4. Spectrometer Control window after connection of the workstation andspectrometer

After data collection, the data is automatically uploaded to the workstation if thespectrometer connection is valid. The data is placed in a file specified by the filenamestring in the experiment header. If the connection does not exist, the data is retained on thespectrometer for a time specified in the machine.config file. The next time aconnection is made to the spectrometer, the data is automatically uploaded. If the processline in the experiment header contains a valid processing program, the program is invoked.

Note: Connection to a spectrometer is necessary prior to scheduling anyspectrometer activities.

Default Spectrometer ConnectionEach user in the.delta_configure file has a Default instrument string. This string isthe name of the spectrometer to which Delta will automatically try to connect when the“Connect” command is given. This string may be changed with the Preferences Tool.

Note: In locations with only one spectrometer, the system is usually set up toconnect to the spectrometer automatically after clicking on the icon.



Select:

after first selecting the spectrometer, to monitor (or observe an experiment on) aspectrometer already in use by another user. The Spectrometer Control Tool changesto look like Figure 4-5.

Note: Only one user can connect to a given spectrometer at a time. However,users from other workstations can monitor the status of the spectrometer. Auser can submit experiments while monitoring the spectrometer. However,those experiments are held in the experiment queue until the current userunlinks.

Figure 4-5. Spectrometer Control Tool in Monitor Mode

Spectrometer Control Tools


Select:

to terminate connection to the spectrometer. Unlink is used to terminate both the Connectand Monitor connections.

to “ping” the network for the status of all Eclipse NMR spectrometers. The node nameswill be listed in the Spectrometer Control Tool window.

Console modeIn console mode -- which acts like a spectrometer superuser -- you have exclusive right tothe spectrometer and can do any of the following:• remove any job from the queue,• change experiment priorities,• write system shim files, etc.To connect to the spectrometer in console mode, select Tools-Mode-Console to bring up awindow into which you enter the password. When a user connects as console, theSpectrometer Control Tool displays this information in the top window, which wouldread:console: nodename not connect:nodename

SPECTROMETER CONTROL TOOLS

Once you have successfully connected to the spectrometer, you may then select fromvarious spectrometer functions and tools using the bottom row of buttons on theSpectrometer Control Tool (Figure 4-6). Most importantly, they make it possible foryou to load a sample and to run an experiment. More information on any one of thesetools can be found by first opening the tool, then consulting online Help.

Figure 4-6. Spectrometer Control Tool Lower Buttons

Select:

To load a sample, lock it, spin it, adjust its shims, etc.



Select:

to start the queue.

to stop the queue.

(For a full listing of menu functions in this tool, consult page 56-5).

To select an experiment, and to modify its variousparameters (header, instrument, acquisition, and pulse).

To open the automation window that lets you automatecollection and processing of NMR experiments.

To activate the swept lock signal display.

To activate the “Real Time” monitor display tool.Note: Once in this View Tool, you must selectthe View Vector button to activate it.

To copy data from spectrometer to workstation while datacollection is in progress.

Select:

Spectrometer Control Tools


SPECTROMETER CONTROL TOOLS

The Spectrometer Control Tools -- Sample, Experiment, Automation,Sawtooth, View and Copy -- are described in order here.

SAMPLE CONTROL TOOL

Figure 4-7. Sample/Shim ToolSelect:

to display, in the Sample Control Tool (Figure 4-7) all the following:• magnetic field strength in Tesla



• cryogen level display, liquid He and N2• physical sample state (Load/Eject)• sample changer slot (optional)• sample spinning state and rate• variable temperature state• lock solvent• lock control• shim controls, and• lock level.

❏ To use the Options menu:Select Options -• Verify on System Shim Modify To ask for verification before modification of the

system shims.• Load Shims from Data File To get the shims by clicking on an open data file and load

them into the Sample Control Tool.

❏ To set up a sample:

1. Set the sample tube (with the sample in it) in the spinner and adjust with the depthgauge. See your NMR administrator for the proper alignment procedure.

Note: When inserting a sample tube into a spinner or removing it, do not applyexcessive force to the sample tube wall. If it is difficult to smoothly insert orremove the sample tube, warm up the spinner by wrapping it up in your hand.This causes the spinner to thermally expand, ensuring easy insertion andremoval.

Warning: Never place an empty spinner into the magnet.

2. Check that the air is flowing by holding your hand over the sample-insertion port ofthe magnet.

If no air is flowing, DO NOT insert the sample tube into the insertion port of the magnet.Another sample may already have been inserted or there might be a problem with the airsystem.

3. Put the spinner containing the sample tube into the sample-insertion port of themagnet and gently release it.

The sample floats on compressed air.

❏ To load samples:Select:

L to load a sample; E to eject a sample in order to load a new one.

Sample Control Tool


• If the flask appears full , and a green light appears above the Sample

Load Icon , then a sample is already loaded in the magnet.

The bar above will turn yellow while the sample is being ejected, green when it has

been ejected.

• The flask is empty when there is no sample loaded, or when the loadedsample has been ejected. When ejecting a sample, be sure to remove the sample fromthe insertion port on the magnet.

❏ Then, to spin the sample and update the display to the new spin rate:

Click on the Spinner .

The sample spinning can be monitored by watching the picture of the top in the Spinner:

• The top will be upright when the sample is spinning.

• It will topple over on its side when the spinning has stopped.

Note: the sample may start spinning automatically, and can be turned OFF by



selecting . The spinner will always turn off when the sample isejected.

❏ Then, to control the temperature:

• To turn temperature control ON, select:

• To turn temperature control OFF, select:

❏ To keep the temperature ON even when the sample is ejected, select:(otherwise, the ON icon will automatically turn to OFF when the sample is ejected).

• The fire blazes when the temperature control is ON.

• It dies out when it is OFF

❏ Next, select the lock solvent from the Solvent scroll list.

(e.g., in Figure 4-7, CHLOROFORM-D was selected). The list of lock solvents iscontained in the solvent.def file on the spectrometer. It is an ASCII file that ismodifiable with a text editor.

• Click on the automatic NMR lock and shim icon: .

• When the NMR lock and shim are complete, “LOCK ON” and “IDLE” will bedisplayed.

Sample Control Tool


Figure 4-8. Lock Control section displays the NMR-lock level Note: to manually shim the sample, use the mouse to maximize the lock level

in the shimming section of the Sample tool (see Figure 4-9).

Figure 4-9. Set the axis for shimming

The magnetic field strength, appearing in a display-only field in the Sample Tool (seeFigure 4-7), is very important to spectrometer operation. All frequencies in Delta areautomatically referenced from the nucleus name (Proton, Carbon13, etc.) For each nucleusa gyromagnetic ratio (gamma) reference value is stored in a file (gamma.def) on theacquisition system. The software multiplies the gamma value by the magnetic field valueto calculate the transmitter frequency. This calculated value also serves as the chemicalshift reference position for each nucleus. Thus, an internal reference (e.g. TMS) is notrequired. This same method works for both Hz and ppm scales. The chemical shift of allpeaks are calculated in this way. The gamma value should never need to be changed.However, samples prepared in mixed solvents, or solvents with high ionic strength, orsamples run at variable temperature may cause the solvent peak to deviate from itsexpected chemical shift (ppm). In these cases, an internal standard may be used.

Shim Tool ControlsShimming serves to homogenize the magnetic field surrounding the sample. The ShimTool Controls display the shim and lock controls.

coarsefineindicators

Lock level



Note: All matrix shims systems have Z5 and Z6. These shim values are useradjustable in Eclipse +. Some systems may have X3 (C3), Y3 (S3) non-spinshims.

The shims are displayed in groups of 4 on the Shim Tool Controls. Below each shimname is its current value and a button pad for shim adjustment. Different groups ofshims may be displayed by clicking on the shim list. The 4 individual shim readoutsmay also be changed independently by clicking on the shim name.

Table 4-1: Shim Tool Nomenclature

Shim FunctionEclipse name GSX name Spherical

harmonic

Magnetic fieldoffset

Z0 FILDC ZO

Spinning shims:

Z1 Z1 Z1

Z2 Z2 Z2

Z3 Z3 Z3

Z4 Z4 Z4

Z5 Z5 Z5

Z6 Z6 Z6

Nonspinningshims:

X X X

XZ ZX ZX

X2 X2-Y2 C2

X2Z Z(X2-Y2) ZC2

XZ2 Z2X Z2X

Y Y Y

YZ ZY ZY

Y2 XY S2

Y2Z Z(XY) ZS2

YZ2 Z2Y Z2Y

Sample Control Tool


Loading Shim FilesShim files for the Eclipse NMR are stored on the acquisition computer system.Because of this it is very easy to reset the shims to a known state. It is also convenientfor the system manager to maintain the default system shim file. Individual usersmay also keep their own private shim files without disturbing the system shim files.

Loading System ShimsSelect:

then to load the “default” or “system” shims for the current probe in themagnet.

Reading in/saving the system shims generates acknowledge windows (Figure 4-10)if the Verify On System Shim Modify option under the Option menu is checked.

Figure 4-10. System Shims Acknowledge WindowThe system shim files are maintained by the system administrator. You must haveConsole privilege (i.e. the password) to overwrite the system shims. The systemshim files are maintained in the /eclipse/probes directory on the acquisitioncomputer. The default shim files are stored by probe code number. There may beonly one system shim file per probe. The system shim files are written in ASCII for-mat.



Loading User ShimsSelect:

then to load a shim file from your own directory. Select the shim filefrom the Open Shim File window (see Figure 4-11).

Figure 4-11. Open Shim File windowSelect:

to save a user shim file back to the directory. Select the shim file from the SaveShim File window (see Figure 4-12)

Sample Control Tool


Figure 4-12. Save Shim File windowSelect:

to print the shims.

to upload current shim values to Delta to ensure the Spectrometer shim

values and Delta shim values are synchronized. When you do this, a message box comesup:

The Lock Level MeterLocated just below the center of the Shim Tool is the lock level meter (Figure 4-13).The top half gives the coarse reading, the bottom half the fine reading. Directlybelow is the numerical lock signal readout. By manually adjusting the shim controlslocated below the meter, you can optimize the amplitude of the lock signal.



Figure 4-13. Lock Level Meter (Minimum 0, Maximum 4095)

Locking the SpectrometerThe lock system may be activated from the Sample Tool Lock Control (see Figure4-14).

Figure 4-14. Lock Control

Figure 4-15. Gradient Shim and Lock ButtonsThe NMR lock system uses the NMR signal from a 2H nucleus in the sample to“lock” the magnetic field frequency. This stabilization uses the Z0 shim coil tocounteract any change or drift in the magnetic field during the experiment. The locksignal amplitude is also used for shim adjustment. A more homogeneous magneticfield will produce a higher amplitude of the lock signal.

The Eclipse NMR lock system requires that the sample have 2H, usually in the formof the solvent, such as Chloroform-D, Benzene-D6, Acetone-D6, etc. The list of locksolvents is contained in the solvent.def file.

The spectrometer may also be run in unlocked mode for samples without 2H or for

performing 2H NMR spectroscopy, by selecting no solvent in the sample toolsolvent list.

There are two things that must be done for the machine to select the correctparameters from a probe file with two entries for 2H:1) the module_config line in the experiment must specify the "lock_switch"

option. This causes the pulse compiler to actually configure the head_amp to use thelock switch device.

Lock Status

Shim Status

Sample Control Tool


2) The machine.wiring file must specify which head_amp circuit is connected tothe lock_switch. This is done by putting a line like the following in the machine.wiring file: "HEAD_AMP(1).out_rf => LOCK_SWITCH(1).in_rf;

(where head_amp(1).in_rf is connected to an LF amp and head_amp(1) actuallyis connected to a physical lock switch.

Select:

To turn on the lock channel circuits. If the spectrometer isin resonance with the lock, it will lock. The lock on buttondoes not sweep the field to find a lock signal.

To turn off the lock channel circuits.Note: this does not turn off the 2H oscillator for2H spectroscopy.

To turn on the lock circuits, increase the lock power andgain, and sweep the field to find a lock signal. After itlocates a signal, the lock power and gain are returned tostandard levels.

To perform autolock and shim.

To perform gradient shim.

To perform gradient shim and lock.

Lock State To display the current lock status. Red is OFF, yellow isWORKING, and green is ON.

Shim State To display the current shim status. Red is OFF, Yellow isworking, and Green is tracking based on the group selected.

Gain To adjust the gain of the lock receiver, set from thesolvent.def file. Autolock will adjust the gain to findthe lock signal.



Monitoring shims and lock signal level and record settingsThe spectrometer constantly monitors the shims and lock signal level and recordssettings corresponding to the highest lock signal level.

If the autoshim is stopped before completion, the spectrometer will execute aLock On. The Lock On will affect the lock level and gain values, but will notaffect the shim values.

Level To adjust the lock channel power level, set from thesolvent.def file. Autolock will adjust the level to findthe lock signal.

Phase To adjust the phase. It is set from the shim file. The phase isa characteristic primarily of the probe and of any RF filtersin the lock channel. The lock phase may change when thedielectric constant or ionic strength of the sample changessubstantially.

Offset To adjust the offset. It is loaded from the solvent.deffile, the Lock Offset is the frequency offset necessary for

the 2H lock signal to set TMS to 0 PPM.

Select:

To clear the previous best shim values.

To restore the shim values corresponding to the highest locksignal level.

The standard autoshim invoked by the spectrometer is Z1,Z2. However, many other combinations are available. Clickand drag on the autoshim input box to activate anotherautoshim combination.

Select:

Queue Management


QUEUE MANAGEMENT

The Eclipse spectrometer is run as a queued device, that is, multiple experiments may besubmitted to the spectrometer. The spectrometer queue has several modes - Owned,Running, Halt, Free, and Waiting. The queue can be altered only from inside the user’saccount.

Each job or experiment in the queue has a priority level. The priority ranges from 0(lowest) to 255 (highest). The default priority is specified in the queue.prioritiesfile on the spectrometer. As a user you can change the priority of your own jobs, but onlyto a lower priority value. Someone with Console privilege can change the priority of anyjob.

The Queue menu on the Spectrometer Control Tool has four options useful in queuemanagement.Select:• Start to resume a stopped queue.• Stop to stop the spectrometer from running jobs.• Reschedule to reschedule a selected job to the end of the queue.• Delete to erase the entire experiment queue except currently running jobs.

When an experiment comes to the top of the queue and is ready for execution, thespectrometer checks the sample name currently in the magnet against that of the newexperiment. If the sample ID is the same, the experiment executes without a pause.However, if the sample ID does not match, or if no sample ID was specified, theexperiment will pause and display a message box on the screen (Figure 4-16). In thiscase, you must select GO.

QueueMode

Queue Control State

Owned When you activate the Connect function and the instrument is free, youown the queue. Although others may submit experiments (theexperiments will be held in the queue), only the connected user'sexperiments will execute.

Running The normal state when another user is running an experiment.

Halted The queue is stopped. When the queue is restarted, all experiments willresume.

Free The queue is free.

Waiting An experiment is pending and waiting for user input.



Figure 4-16. Acknowledge message windowAn experiment pending in the queue will resemble the one in Figure 4-17. Notice the’-’on the top line.

Figure 4-17. Spectrometer Control with Experiment Pending

After selecting the experiment, and selecting Start from the Queue menu, the queue willresemble Figure 4-18. Notice the’-’ has changed to a’*’.

Figure 4-18. Spectrometer Control with Experiment Running

Experiment Data

PriorityEach experiment has a priority ranging from 0 to 255. A user can change priorityonly to a lower status. The Console has privileges to change any priority.

pending

running

Queue Management


SlotThe slot parameter is used only with a sample changer.

Job Start TimeNormally, experiments are placed in the run queue immediately after submission.However, an experiment may have a delayed start time. The Job Start Time is thetime the experiment is placed in the run queue, not necessarily the time when it startsrunning.

Additional Experiment InformationIf you “double-click” on an experiment in the queue list window, an information windowwill appear on the screen (Figure 4-19). The window contains information related to theexperiment.

Figure 4-19. Experiment Information Window

4. If the parameter you want to confirm is not in view, scroll the screen by clicking on theup ▲ or down ▼arrow until it appears.

5. To close the window, click on the Finished button.

Note: You cannot change an experiment’s parameters once it is in the queue.

Deleting Queue items

Deleting a specific queue itemYou can remove a measurement from the queue as follows:

1. Click on the item you want to delete from those displayed in the Spectrometer Controlwindow.

The specified queue item becomes highlighted.

2. Click on the STOP button in the Spectrometer Control window.

The confirm window opens, asking whether or not to delete the queue item.



3. To delete the queue item, click on the OK button.

Deleting all queued experiments

1. Move the mouse pointer to Queue in the tool bar in the Spectrometer Controlwindow, and press and hold down the mouse button.

A pull-down menu appears.

2. Move the mouse pointer to Delete and release the mouse button

The Confirm window opens, asking whether or not to delete all the queue parameters.

To delete all the queue parameters, click on the Ok button.

EXPERIMENT TOOL

The Experiment Tool stores, creates, and compiles the pulse sequence and parameters.The Experiment concept combines pulse sequences and parameter files into a single unit.The entire experiment is stored with the resulting data and may be extracted and re-run.

An experiment has four basic parts: Header, Instrument, Acquisition, and Pulse.From the Spectrometer Control Tool, it is possible to run an experiment.

For information on how to write and modify experiments over and above whatthe following section provides, please consult “Experiment Tool and EclipseExperiment Programming” on page 10-1, “1D NMR Measurement” on page 4-

Experiment Tool


1, and “2D NMR Measurement” on page 5-1.

Experiment Selection

In the Spectrometer Control window, select :

to access the Open Experiment window (Figure 4-20). You may use this window toselect an experiment.

Figure 4-20. Open Experiment Tool

Local Experiment DirectorySelect:

to list your local experiments. The user's local experiments directory is specified by theExperiments string in the.delta_configure file.

Global Experiment DirectorySelect:



to list the global experiments. The system global experiments directory is located as a sub-directory in the Global string in the.delta_configure file. In this directory, thestandard files supplied from JEOL are stored. Its files cannot be changed. TheseExperiment files contain the measurement modes, standard measurement conditions, andprocessing operations to be carried out.

Loading an ExperimentThe experiment loads as a single window containing all parameters necessary for aparticular experiment. It is divided into four parts, which you can either select with iconsor scroll to.

The Header SectionThe Header section (Figure 4-21) is used for the sample_id, filename, comment, etc.However, it has two other major functions. First, the process section of the Headerspecifies what processing, if any, is to be done with the data after collection. Second, theHeader section has experiment flags. The experiment flags control various spectrometerand data collection features. The experiment flags can be added dynamically by clickingon the Header button. (See Adding Header Flags and Parameters Dynamically in Chapter10 or page 4-3 in the Delta Tutorial for more detail.) The parameters added will be usedfor the current experiment only.

Experiment Tool


Figure 4-21. Experiment Header Section

❏ Set Hints in the Options menu to show buttons to set experiment parameters.Click on the parameter name to bring up an edit window. Not all parameters have an editwindow.

❏ Select the Edit button to customize data handling:The Set process window allows you to customize the way the data is treated after theexperiment is completed (see Figure 4-22).



Figure 4-22. Set Process WindowTo edit the process command line, click on the Edit Button to bring up the Set Processwindow which allows you to set the process parameters for the experiment. The input boxlists the name of the program or macro to be invoked when data collection is completed. Ifit is left blank, the data is simply written to disk.

Use the horizontal row of buttons at the top of this tool to start the processor appropriate tothe selected data:

Experiment Tool


Process lists may be created directly from data processors.

The Instrument SectionThe Instrument section (Figure 4-23) contains instrument-related hardware conditions. Acomplete listing of instrument parameters is given in Appendix B, “InstrumentParameters,” or can be viewed using the Params button on the Spectrometer ControlTool.

❏ To add additional instrument parameters:Click on the Instrument title (a button may or may not be visible). (See “AddingInstrument Parameters Dynamically” on page 10-26, or page 4-4 of the Delta Tutorial.)The parameters added will be used for the current experiment only.

Select:

Process_nDimensional...Process_Interactive_Global

To process data from the source specified.Process_Interactive brings up the process 1D or nDwindow, Process does not.Process_Local will (behind the scenes) process the datafile using the supplied processing list in the localprocessing list directory.Process_Interactive_Local will pop up the window andload the processing list found in the local processing listdirectory.Process_Global (behind the scenes) will process the datafound in the global processing list directory.Process_Interactive_Global will pop up the window andload the processing list found in the global processing listdirectory.

Send_data_to_finger To send collected data to a process you have fingered.

Other () To type a user-defined processing program.

Get Process List To opens a window allowing you to specify the user-defined or global processing list.

Clear Processing list To remove the processing list filename from the command.

Accept To place the command into a process parameter.

Cancel To cancel the setting.



Figure 4-23. Experiment Instrument Section

The Acquisition SectionThe Acquisition section (Figure 4-24) contains the acquisition parameters, providinginformation about the NMR frequencies, sweep widths, data points, etc. In certainparameter fields, you may enter only a single numeric value (in some cases, multiplevalues). See page 4-5 in the Delta Tutorial for a discussion of setting Acquisitionparameters.

Experiment Tool


Figure 4-24. Experiment Acquisition Section

The Pulse SectionThe Pulse section (Figure 4-25) contains the virtual parameters needed for the pulsesequence. See “Pulse Section” on page 10-29 and page 4-6 in the Delta Tutorial for moredetailed information.



Figure 4-25. Experiment Pulse Section

❏ View pulse sequences by clicking on the Pulse title.A pulse viewer will pop up on the screen (Figure 4-26).

Any changes made to a particular experiment can be saved for future use in theuser’s home directory. To do this, select Save from the File menu.

Any changes made will NOT affect the default values from the global directory.

Experiment Tool


Figure 4-26. Pulse Viewer



AUTOMATION WINDOW

❏ To open the Automation Tool: (Figure 4-27), Select:

.

Figure 4-27. Automation Tool

Automation Window


❏ Use the Automation Tool to automate NMR experiments.With this tool, you can collect, process and present data. It lets you submit a series ofexperiments, or pass parameters from previous experiments for use in a subsequentexperiment. When the Automation Tool is opened, it automatically checks the localtemplate directory for the default file -.delta_automation.auto. If this file is notfound in the local directory, the global template directory will be checked. If no default fileis found in either directory, the tool will be opened and left empty.

The File menu (see also page 14-4) lets you load (or remove) a methods file, save it as thedefault file, look at the automation queue, or start the Automation Editor (Figure 4-30).Use the File menu also to access the LC-NMR Method Queue. This tool is described inthe User’s Reference Guide (study this material in “LC-NMR Method Queue” on page 34-

Select:

To load a new methods file and remove all currently loadedmethod files.

To load a new methods file without removing currentlyloaded method files.

To show the Automation Queue (page 4-37).

To hide the Automation Queue.

To invoke the Automation Editor (page 4-39).

Note: If the single line separating theexperiment buttons is clicked, it will changeinto a double line. This will cause theexperiment file right below the double line to beloaded into the Automation Editor when it isopened.

To inform the instrument that it is OK to run experiments.



1).The Sample menu lets you load or eject the sample.

Note: The first time a sample ID is used in an experiment automation, amessage box will pop up to remind you to load the sample. Click the OKbutton after loading the sample to continue the experiment.

❏ To run an experiment, first fill in the following information:

Filename Supply a sample filename. In some cases, where there is noSample ID field, this parameter is used for the Sample IDas well.

Comment Enter your comment for the sample.

Slot Select a number for the sample changer slot for the nextexperiment. Use zero for no sample changer.

Temp. Set Select the temperature desired.

Temp. State Select from Temp On/Temp Off to turn on/off theautomatic temperature control.

Solvent Select a solvent from the list.

Notify: When an automation is complete, e-mail notification willbe sent to the addresses specified.

Sample Status Shows if there’s a sample loaded in the spectrometer.

Curr. Temp. Gives the current spectrometer temperature.

Lock Status Gives the current spectrometer lock status.

Method buttons Select from the method buttons at the bottom of the screen.Doing so will submit all experiments in that method to theautomation queue. Use the right mouse button to see thehelp on that method.

Automation Window


Automation Queue

Figure 4-28. Automation Queue Window

❏ The Automation Queue window lists experiments in the order they weresubmitted.The first experiment in the queue will be highlighted in green (if, for any reason -- e.g., asample with the wrong lock solvent is inserted into the spectrometer -- this experimentwill be bumped, it will appear in red at the bottom of the list.) The scissors button lets youcut a single method from one place in the queue, to paste it (using the paste icon) inanother. Use the Remove button to remove a selected experiment from the queue. You canalso save a particular queue to your home directory, by selecting Save Queue in theOptions menu. Options-Print Queue lets you print the contents of the queue.



AUTOMATION CONSOLE

Figure 4-29. Automation ConsoleThe Automation Console (Figure 4-29) acts as a dummy terminal to simplify datacollection for users who don't need the full functionality that the Delta Console provides.It combines features of spectrometer selection and control with automation features andsample monitoring. For a more complete description of this tool, see Delta User’sReference: “Automation Console” on page 15-1 (or online help). See also “LC-NMRMethod Queue” on page 34-1. Essentially, it combines features of the SpectrometerControl Tool, the Sample Control Tool and the Automation Tool.

Note: In order for this tool to come up automatically when you start upDelta, the DELTA_CONSOLE preference needs to be set by the system

administrator to automation_console, or it needs to have automation_consoleas an element in a set of elements (see Appendix E in the Delta User's Guide).Note also that this tool has a user-defined menu option described in AppendixE, p. 46.

SamplePreparation

MethodSelection

Spectrometer control Sample monitoring

Automation Editor


AUTOMATION EDITOR

Figure 4-30. Automation Editor

❏ To invoke the Automation Editor (see Delta User’s Reference: “AutomationEditor” on page 4-39):• Select Automation Editor from the File menu of the Automation window.• Or Select Automation Editor from the Acquisition menu of the Delta Console.In this scrolling window you can edit any of the parameters for automatically running allthe experiments in any of the methods in the automation template file. Its usage is morefully detailed in on-line help or see Delta User’s Reference: “Automation Editor” onpage 13-1.

Select:

To open an automation template file.



To open a new automation template file and combine itwith the current automation template.

To save the automation template file.

To bring up the Edit Sample window to edit the defaultsample list.

Note: The parameters entered in the EditSample Window will only be used if the selectenumeration next to the parameters found in thesample section is set to Sample.

To display the Dependency Graph of the experimentsin a selected method.

To bring up the Presentation window to customize theway data files will be plotted after each group is run.

To jump to the Method section.

To jump to the Group section.

To jump to the Experiment section.

Select:

Automation Editor


Methods for Customizing Automation

It is important to understand the Automation Editor. As the flow chart belowexemplifies (see Figure 4-31), you can run multiple experiments and print their outputstailored to your needs with a single click of a button. You can also forward parametersfrom a previous experiment in a group to successive experiments within the same group.

Passing (or forwarding) of information from one experiment to another is onlypermitted within individual groups.

To jump to the initialize/forward section.

To jump to the sample section.

To remove the selected item from the list and store thecontent in the paste buffer.

To paste the content of the paste buffer.

Select:



Figure 4-31. Flow Chart for an Automation Editor

The Automation Editor allows you to generate methods to customize automation in amulti-user environment. This structure is reflected in the design of the AutomationEditor. With this editor you can cut and paste a method and all associated informationinto another automation file.

A method consists of groups which in turn contain experiments.

The method name identifies its purpose in the Automation Tool. Name length islimited to 25 characters; truncation is automatic.

• Ctrl-click will turn the input box green and allow the user to change/edit the name.• Alt-Click will deselect the item in the list box.

Groups ensure flexibility, even from the quality control standpoint. Each group is capableof executing a Percival program upon its completion. There are three predefined Percivalprograms that can be run:• dept_automation --> automatic subspectra• dept_filter {x,y,z,a}: where x,y,z,a are 13c, Dept 45, Dept 90 and Dept 135

respectively• phase_automation --> phase of 2D phase-sensitive data.

Experiments are executed sequentially. Each experiment must have an experiment fileassociated with it. In addition, the data file returned after completion of an experiment hasto be processed if an output is required. The necessary processing list is placed in the fieldthat requests a process file. It is important to note that a single returned file can beprocessed using multiple process files.

All experiments in one Method name

Group namePROTON CARBON 2 DIMENSIONAL

single pulse homo_gated 13C APT DEPT 1H 13C COSY HETCOR

PRESENTATION PRESENTATION PRESENTATION

Exp. name

Lock Signal Display - Sawtooth


For automation in a multi-user environment, it might be necessary to reset the shims to adefault value. The shim file field accommodates this feature. From an automation point ofview, it is recommended that this option be invoked only for the first experiment in agroup.

Use Forward/Initialize to customize the parameters of an experiment at the time ofexecution. Any parameter you initialize will override the parameter in the experiment.This allows for changing instrument and user-defined parameters. For a list of commonparameters, click on the parameter button.

Forwarding parameters is of great importance when acquiring 2D data sets. For ease ofuse, the commonly used forwarded parameters are available as pushbuttons. In addition,the forwarded parameters can be constrained using >, >=, <, <=, Multiplier and Mod.

Sample lets you control certain features so that they are non-modifiable. As an example,temperature control can be disabled for the front-end user. If a value is:

• Runtime controllable, editing is allowed when submitting an experiment.• Fixed, the parameter is not modifiable.• Sample. If a sample is specified in the group section it will use the value that is in the

sample definition.For more detail, see Delta User’s Reference: “The Logic of Automation Editing” onpage 13-7.

LOCK SIGNAL DISPLAY - SAWTOOTH

Sawtooth derives its name from the wave form used to drive the Z0 shim. The shim coilsweeps the magnetic field over the Sawtooth Range. If the lock signal is in the range, asignal will be observed. Often the Lock Gain and Lock Level must be increased toobserve the lock signal. However, they may need to be lowered after the signal is locatedto prevent saturation.

Select:

to activate the swept lock signal display. This display may be used to locate and observethe lock signal (Figure 4-32). Normally, it is not necessary to run Sawtooth on everysample unless there is a problem with the autolock function, or unless the sample locksolvent composition is unusual (i.e. 10% D2O, or mixed solvent). In Monitor mode, this

function is not allowed.The Sawtooth runs a separate experiment that appears in the queue in the samemanner as any other experiment. Because of this there will be a pause todownload the pulse sequence and trigger the first acquisition. Data will notappear in the SAWTH window until the first acquisition has finished. It ispossible to shim on the lock signal simply by using the Sample Tool whileSawtooth is running. Pressing the button marked Cancel Sawtooth will cancel



this procedure.

Figure 4-32. SAWTH or swept lock signal display

VIEW TOOL

Select:

to activate the “Real Time” monitor display tool (Figure 4-33). This tool will display thecurrent summed data from the acquisition processor.

This data is shown in “Real Time” at the interval specified by the “mod return”parameter in the Experiment acquisition section.The View Tool display may not be able to keep pace if the data set is too large,the acquisition time and relaxation delay are too short, or if the network load istoo great. Data is not lost in this case.The View Vector Speaker button must be pressed to activate the View Tool’sdisplay. After 5 minutes of activity the View Tool will deactivate (gray-out)automatically. This feature is to prevent accidental overloading of the networkwhen operators inadvertently leave the View Tool open. To reactivate the ViewTool, press the View Vector button again.

When the View Vector Speaker button is toggled to this setting , you can

hear the sound of a FID: Hear the data while you are collecting it!

View Tool


The View Tool may be used to shim on the FID with either the Shim Tool or thespectrometer sub-operation unit (i.e. knob box). Set the Repeat flag to TRUE in theHeader Section of the Experiment Tool to do this.

Under the Processing pull-down menu is an Abs Intgrl command. This option willcalculate the absolute value of the integral and display the log10 of the integral.

Under the Processing menu, you may apply several processing steps to the FID. Press theProcess Vector button to display the current vector processed according to the checkboxes in the Processing menu. When the display mode or processing mode is changed, thedisplay will not update until the next acquisition vector is received.

For more information, see Delta User’s Reference: “View Tool” on page 63-1.

Figure 4-33. View Tool -- raw data



Figure 4-34. View Tool - processed data

COPY

Select:

to copy data from the spectrometer to the workstation while data collection is still inprogress. All the accumulated data will be returned.

If the acquisition rate is too fast, Copy may terminate the experiment.Note also that you may control the availability of the Copy function,disallowing copy, by default, for automation experiments. To do this, select theallow_copy experiment header parameter in the header parameter list thatpops up when you select the Header title in the Header window.


CHAPTER 5: PROCESSING 1D DATA

INTRODUCTION

This chapter will cover the basic steps and an approach for processing one dimensionalNMR data with Delta software using the 1D Processor -- including procedures for:• Start-up (page 5-4)• File selection (page 5-4)• Processing list construction (page 5-7)• Mouse Cursor (page 5-19)• Level Tool (page 5-59)• Data Geometry Options (page 5-60)• Spreadsheet (page 5-64)• Presentation Manager (page 5-69)• Simple mode processing (page 5-78).A detailed walkthrough of 1D is found in the Delta Tutorial, beginning on page 4-1.

Figure 5-1. 1D Processor

Chapter 5: Processing 1D Data


1D PROCESSOR

❏ Use the 1D Processor (Fig. 5-1) to process one-dimensional data.This section will not cover all features of the 1D Processor. It will cover onlythe basic steps of 1D processing. For a more detailed discussion of menus andtools, see Delta User’s Reference: “1D Processor” on page 7-1.

Since the Mouse Cursor Tool (page 5-19; and Delta User’s Reference:“Mouse Cursor Tool” on page 4-1), Level Tool (page 5-59; and Delta User’sReference: “Level Tool” on page 5-1) and Presentation Manager (page 5-69; and Delta User’s Reference: “Presentation Manager” on page 46-1) areused extensively in manipulating data in Delta, their usage in 1D Processingwill be introduced briefly later in this chapter; these tools are more fullydescribed in the Delta User’s Reference Guide.

The 1D Processor will have two data display areas when the Show FID toggle in thePreferences menu is enabled:• The upper area displays untransformed data.• The lower area displays processed data.Icons (including user-redefinable processing algorithms), menus and labelled buttonscontrol the processing. The 1D Processor also has specialized widgets for phasing (P0,P1, PP in the lower right hand corner of Figure 5-4).

Figure 5-2. 1D Processor with untransformed and processed data

inputarea

outputarea

1D Processor


The 1D Processor display window format is controlled by the Show Toolsand Show FID options under the Preferences menu on the menu bar. ShowFID will show only the original data in the file; hence, if the file was savedwith transformed data, the “FID display area” enabled by Show FID will notcontain a FID, but the transformed data set!

In addition, the 1D Processor Tool has two modes:• a “Simple Mode” for basic push-button processing (page 5-78), and• an “Extended Mode” for both basic and advanced processing.

Default Start-up Mode

You can set the default start-up mode for the 1D Processor by using thePreferences Tool. Normally, Extended Mode is the default start-up mode.But if the PROCESS_ONED.SIMPLE_MODE parameter in the.delta_configure file is set to TRUE, then the Simple Mode will be thedefault.

To switch between Simple and Extended modes while running DELTA:select or deselect Extended in the Preferences pull-down menu from the 1DProcessor Window Menu bar.

To save the selected mode so that it is invoked the next time: choose SaveExplicitly in the Preferences menu.



1D PROCESSOR START-UP PROCEDURE

❏ To load data into the 1D Processor:

• Select from the Delta Console Tool Bar, or• Processors, then Process 1D (^1), on the menu bar.

• If you start the 1D Processor by selecting , the first window to appear is anOpen File Tool with the title Open Data for Processing (Figure 5-3).

Figure 5-3. Open File Tool Window

The Open File Tool

❏ The Open File Tool Window has several parts:• At the top left is the current directory name. Use the mouse to select and then edit

this string.• At the top right is the input file filter, a string that restricts the list of displayed files to

those that match the filter. An “*” will show all files (i.e.,.DAT,.TXT, etc.). Use themouse to select and then edit this filter.

• On the left side is the list of subdirectories in the current directory. The “..” symbol isthe next directory above the current directory.

• Use the directory icons to initiate data file selection:

• File information and file name fields contain the specified information.• The center column lists files in the selected directory. The bars to the right side of each

column are scroll sliders. Use the mouse to scroll the display.• The right column contains the file version number. Delta supports multiple file

versions by appending a number to the end of the filename.

Input File Filter

File VersionNumber

CurrentDirectory Name

List ofSubdirectories

List of Files

File Info

Name ofSelected File

Directory Icons

1D Processor Start-Up Procedure


Delta never processes or destroys the original data set. Before any data set isprocessed, a copy of the data is made with the same filename, but a differentversion number. When you save a data file, the data is written to disk with thesame filename, but the version number is incremented. Because some copies ofthe data are used and then deleted during processing, it is common to have gapsin the version number list.If you do not select a file version number, the most recent (highest number)version is assumed.

❏ To select a 1D data file from the Open File Tool:1. Browse the directories to select the file to be processed.

2. Choose a file from the list of files, and a version number from the file versionnumbers to the right.

If you do not specify the version, the latest version (the one with the highest versionnumber) is selected.3. Click on the OK button.The Open Data for Processing window automatically closes and the1D Processorwindow opens.

Note: If you decide not to load data, click on the Cancel button.

Select:

To display all hidden files and subdirectories in the currentdirectory. By default, these files are not shown.

Click this icon once for local directory and twice for localhome directory.The Open File tool will list the directory specified by theDATA entry in the .delta_configure file.

Click this icon once for the global directory and twice forthe global home directory.The Open File tool will list the directory specified by theGLOBAL entry in the .delta_configure file.



1D PROCESSOR WINDOW - EXTENDED MODE

After selecting a data file from the list in the Open Data for Processing window andselecting OK, the red outline of the 1D Processor window will appear on the screen.Use the mouse to position the window, clicking the mouse button to place the 1DProcessor window (Figure 5-4). You can change the position of the window or size it atany time using the mouse. The 1D Processor window title bar will then display the nameof the selected data file.

Selecting the Process 1D command from the Processors menu in the DeltaConsole will open a blank 1D Processor window with only Process 1D in thewindow title bar. You must then call the Open File Tool yourself. Note alsothat if you select a file of greater than one dimension, an nD Processorwindow will be required to process it. The nD Processor will be invokedautomatically.

Figure 5-4. Extended Mode 1D Processor after Performing FFT and Phasing

Note: For a quick reminder of any icon button function, simply select thebutton with the right cursor button.

Data Source Radio Toggle Buttons

1D Processor Window - Extended Mode


Processing ListsThis Processing List illustrates the basic concept of the Extended Mode 1D Processor. Ittakes the data from the input (upper) window area and outputs it, processed, to the lowerwindow. For example, the data in the lower window of Figure 5-4 has undergone FastFourier Transform (FFT) and phasing.

Figure 5-5. 1D Processing List

Processing lists may be obtained in two ways:

❏ To recall a processing list from disk:Select File - Open List from the 1D processor menu bar. Then, in the same manner youselected a data file from the Open File window, select a processing list from the OpenProcess List window (Figure 5-6).

List display area

List pointer (*)

Scroll bars

Open Processing List

Save Processing List

Selected item

Process List SourceRadio Toggle Buttons



Figure 5-6. Open Process List window



The list you select will be read directly into the List display area illustrated above (Figure5-5).

Note: A Processing List may also be saved to disk.

❏ To build a new processing list using icon buttons and menu commands:Select processing algorithms - operators - from pulldown menus under the menu bar, andfrom the double row of icons. As you select them, they become part of the processing list.

❏ To select an operator from the menu bar:1. Select a menu on the 1D Processor.2. Holding the mouse button down, drag the mouse to highlight the desired option or

command. Certain operators require that arguments be supplied.3. Release the mouse button and the option will appear in the processing list.

Note: Processing lists may also be edited by user-modifiable macro buttons (thesecond row of icons).

Note: 1D Processing Lists always end with the[display/phase]statement. This statement always appears at the end of the list and cannot beremoved.

❏ To edit any processing list in the List Display area:Select from the set of pushbuttons in the upper right of the Extended 1D Processor.Certain buttons control how the processing list is assembled:

Select:

To apply the processing list to the input data each time achange is made to the processing list or the list parameters.Auto Process may be CPU-intensive, depending on thelength and complexity of the processing list and data set.

To apply the processing list to the input data and display theresult in the output window.

To place the next processing item at the end of the currentprocessing list. Even if a processing step is highlighted, thenext selected item will be placed at the end.

To place the next processing item before the selected item.This allows you to insert new operations anywhere in thelist.

To change a selected (highlighted) item to the next itemselected from the pull-down menu or the macro button.



Note: Any particular function should only appear once in a given processinglist. When you add an item make sure that you delete any previous occurrencesof that item.

❏ A Sample 1D Processing ListYou create a processing list (see below) by selecting processing algorithms in the orderdesired from the menus in the 1D Processor. For example, you might select:

• DC_balance from the Pretransform menu.• Single exponential from the Window menu.• FFT from the Transform menu.• Machine Phase from the PostTransform menu.• PPM from the Display menu.

Then select to process the data.

Extended Mode Icon Buttons - Top RowAt the top of the 1D Processor are icon buttons used for retrieving, loading, saving,printing, and automatically processing data. This row is also used in the Simple mode.

Note: DELTA can retrieve data from different sources. See below.

To cut the selected line from the processing list.Note: Cut and Paste are local to the processing list.

To paste a cut item at the selected location in the processinglist.

To clear the whole processing list.

To delete the currently selected (highlighted) item in theprocessing list. All items following the deleted item will berenumbered automatically.

Select:



Select:

To open data files from disk. This is the most common datasource.

To load a data file from another geometry.

Note: One or the other of these two buttons is always selected(depressed), so, in effect, these buttons toggle.

If the 1D Processor is already running, load new data byselecting either this Open File folder icon or Open File(^O) from the File menu. The source of the new file isdecided by which icon is depressed - the disk icon or thefinger icon.

Select this Open File Clear icon or Open Clear from theFile menu to load a new 1D file and remove the currentprocessing list. The source of the new file is decided bywhich icon is depressed - the disk icon or the finger icon.

To export the current geometry into the Data Slate (seeChapter 6).



To save processed data to disk. This window will appear.

Figure 5-7. Save Data File windowThe filename will stay the same, the version number will beincremented by 1.

To plot the processed file.

To print a spreadsheet with all the peak information.

To automatically peak pick the data.

To automatically integrate peaks by measuring and cal-culating a running sum for the area underneath selectedpeaks.

To automatically peak pick and integrate the spectrum.

To compute the file statistics and update the geometry withthe new file. These statistics include positive and negativethreshold values, noise, baseline, minimum and maximumintensities.

Select:



Extended Mode 1D Processing Icons -- Second RowThe most common processing functions can be selected by clicking on the second row oficon buttons located at the top of the extended 1D processor. These buttons -- each ofwhich has a default given in the table below -- may be redefined to related standard 1Dprocessing functions by the user.

Note: It is also possible for the user to define a macro to meet the special needsof an experiment set.

To autophase the spectrum.

Select:

To redefine any macro, click on Define, then on the macroicon. Select the new process(es) from the list of Operators.The new macro is memorized only for that session unlessSave Explicitly is selected in the Preferences menu. Youcan use the buttons to cut from, paste to, append or insertinto, or remove an operator from the list. Apply applies thechange, Cancel cancels it.

To remove stray zero frequency peaks that may be causedby a channel imbalance in the FID due to a difference in theDC Balance.

To apply a Hamming window function to the file. Thisbutton can be reset to apply any of these Window functions:Double Exponential, Gauss, Hamming, Kaiser, SingleExponential, Sinebell, Sinebell Automatic, Sinebell (order2), Sinebell (order 4), Sinebell Shift, Traf, Traf Modified,Trapezoid3.

To perform a Fast Fourier Transform (FFT) on the file totransform the data from the time domain to the frequencydomain. This button can be reset to include any of theTransform functions: FFT, Hilbert, IFFT, MaximumEntropy, Transpose.

Select:



MENUS FOR EXTENDED 1D PROCESSING

This section discusses Pretransform (page 5-14), Window (page 5-17), and Transform(page 5-17) functions.

PreTransform FunctionsThe PreTransform menu contains various operations done before the FFT. Only two --DC Balance and Zerofill -- will be discussed here. Please consult the DELTA User’sReference Guide for a discussion of the other PreTransform menu functions (page 5-14).

To apply user-defined phasing. This button can also beredefined to apply Automatic Phase and/or MachinePhase.

To correct for errors found in the baseline of frequencydomain spectra. This button can be redefined to apply anyof these PostTransform functions: Base Correct,Base_correct (Interactive), DC Correct.

To take the absolute value of the file and reduce the file tothe size of the real only data. Alternatively, this buttoncould be defined for the Symmetrize function.

To translate the data into parts per million (PPM). Thisbutton could also be defined for Hertz or AutomaticReference rulers.

To peak pick the data file. This same button can be used toapply Peak Pick/Integrate, Apply Integral or Print peak listprocessing to the file.

To plot the spectrum and its parameter information. This isa predefined macro button. Only operators from apredefined set can be used in this macro (see page 5-10).

To use a user-defined processing macro.

Select:

, ,

Menus for Extended 1D Processing


DC BalanceThe DC balance function calculates any DC (constant) offset between the real andimaginary data channels. An imbalance between the channels causes a “centerspike” or “zero frequency glitch” in the transformed data.

ZerofillThe Zerofill function extends the data set with zeros by the number of timesspecified. All dimensions must be a power of 2 and will be automatically zerofilledto the next larger power of 2. Therefore the number of times specified should be apower of 2, i.e. 1, 2, 4, 8, 16, etc. If a number is entered which is not a power of two,it will be rounded to the next highest power of two.

Note: A zerofill of 1 will leave the data unchanged. The Zerofill operator takesone argument. When Zerofill is selected in the processing list, the input boxbelow the processing list will contain the argument (see Figure 5-10).

❏ To change the value of zerofill:1. Place the mouse in the input box. The mouse pointer will change to a text cursor.2. Using the Backspace key, delete the entry and type a new argument.



Example:Begin with an empty processing list as shown in Figure 5-8.

Figure 5-8. Empty Process ListUsing the mouse button, select PreTransform and then drag down to DC Balanceand release. DC Balance will appear in the processing list as shown in Figure 5-9.

Figure 5-9. Process List after Adding DC balance

Again using the mouse, select PreTransform and then Zerofill. Zerofill will beentered in the processing list after DC_Balance, and the default number of times willbe displayed in the input box. Change the number from 1 to 2. The processing listshould now look like Figure 5-10.

Figure 5-10. Process List after Adding DC Balance and Zerofilling



Window FunctionsWindow or apodization functions are used to enhance or to emphasize features in the data.The most common is the single exponential window function (Single Exponential).Another common apodization window is the Sinebell. The Sinebell apodization windowis available in several variations.

Single ExponentialSingle Exponential applies a single exponential with a user-adjustable broadeningfactor. The line-broadening factor is adjusted to approximate the decay of the FID.Line broadening has units of Hz. Use the input box to modify the broadening factor.

Example:Select Window on the Menu Bar and drag the mouse to Single Exponential.Release the mouse button and sexp will appear next to the end of the processing list.Change the broadening factor by editing the input box. The process list should nowlook like Figure 5-11. To process the FID with the new entries in the processing list,

click on .

Figure 5-11. Process list after adding Window function

Transform FunctionsTransform functions are used to convert data from one type of domain to another. In thismanual, only the Fast Fourier Transform (FFT) and Maximum Entropy will be discussed.Please consult the Delta User’s Reference Guide for a discussion of other Transformmenu functions (page 7-19).



Fast Fourier Transform (FFT)Applies a Fourier transform to the input data, converting it from a free inductiondecay (FID) in the time domain (units in seconds) to a spectrum in the frequencydomain (units in Hertz or PPM). FFT has an optional parameter that is the multiplierfor the first data point of the data prior to the transform. This feature may be used tocorrect for baseline distortion due to incorrect sampling of the data. The multiplieris normally set to 1.

Example:Select the FFT option from the Transform menu with the mouse. The FFT will beentered in the processing list as shown in Figure 5-12. Click the Process button toapply the FFT to the data and display the result in the lower window.

Figure 5-12. Process list after adding Fast Fourier Transform

Notes on Maximum EntropyMaximum Entropy attempts to use the maximum entropy principle in order to reconstructa spectrum. The entropy used to regularize the spectrum is the entropy function derivedindependently by Daniel and Hore (JMR 84, 1989) and Hoch and Stern (JMR 86, 1990):

This entropy functional can be demonstrated to be appropriate for the regularization ofMR spectra of spin 1/2 particles. b is a normalization constant that strictly should be setfor the integral over all space of the number of spins with a particular shift and orientationin the sample. In general, setting b to a small value is appropriate.

Two other optional parameters to Maximum Entropy are Times, the number of points inthe reconstructed spectrum divided by the number of data points collected; and Noise, anestimate of the noise value of the data.

The spectrum is then reconstructed by determining Mω which minimizesS - λ C (where C is the chi squared value of the reconstructed spectrum with respect to theoriginal spectrum).

S12---

M ω( )b

----------------- M ω( )

b-----------------

1 M ω( ) 2

b2--------------------–

1 2/–asinh

ω∑–=

Cursor Tool


Since PostTransform and Display menu functions require using the Cursor Tool,discussion of these menus will follow that tool’s introduction.

CURSOR TOOL

Because of the wide array of operations used to manipulate data geometries, a specialcursor tool was developed to perform data operations. Here, we will discuss only basicusage of this tool (its operations are spelled out in more detail in the (Delta User’sReference: “Mouse Cursor Tool” on page 4-1)). The example here is based on data

loaded in a Data Slate (accessed by selecting the button on the Delta Console). Note: The new cursor buttons replace the older cursor tool which had its own

separate window. Located in the upper right of the active data geometrywindow, the cursor tool (illustrated below) is created automatically whenever ageometry, with data, is opened. If you are working with more than onegeometry open, the cursor tool will move from window to window as youreposition your cursor.The Cursor Tool is created whenever a geometry with data is opened if the line“CURSOR_TOOL_ON = TRUE” appears in your .delta_configure fileor if the Cursor Tool is toggled ON in the Preferences Tool. This is the defaultsetting.

Figure 5-13. 1D Zoom mode operations

1D Zoom mode operations



❏ To use the Mouse Cursor Tool, select:1. The loaded 1D data geometry you want to work with.

Note: to load a data file, use one of the File - Open menus.

2. The Tab in the upper right hand corner of the data geometry to open or close theMouse Cursor Tool.

3. The cursor Mode (by name) that you want to use on the data. To change modes, clickon the mode name.

Note: You can also use function keys to change modes.

4. An operation from the picture buttons. These operations -- detailed in the Delta User’sReference: “Cursor Operations” on page 4-4 -- may differ according to the geometrytype.

5. Select for a list of Keyboard commands. These keyboard commands vary withthe cursor mode, and with the data view (flat, stack, spatial). A list of these keyboardcommands can be found in the Delta User’s Reference: “Keystrokes and KeyboardCommands” on page 4-35. You can use these commands in analyzing geometries -- inintegration, j-coupling, normalizing, creating peaks, changing a file’s reference,zooming, and sequence analysis. Some of the more commonly used techniques areelucidated in this chapter.

❏ When the geometry window is quite small, only the current operation may bevisible.In this case, other operations are listed in a pull-down menu under the mode button. Othermodes/keys can be selected from the popup menu accessible from the right mouse button.

Note: Select spacebar to move right through the list of operations; shift-spacebar to move left through the list.

❏ In some instances, no mode button appears:Note: When, as in the Presentation Manager, the Cursor Tool Tab button is notvisible:

- change cursor modes using the function buttons (F1 to F12).- use the spacebar to move to the next cursor operation.- use shift - spacebar to move to the previous operation.

Mode

KeyboardKey Commands

Tab

Operations

Cursor Tool


Note: The mouse cursor tool is customizable in the Preferences Tool. Thisis true for every operation and for every mode.

To change display attributes for a display area using the “accelerator key”functions, you must have the “Input Focus” in that display area.

Figure 5-14. Sample Key command menu6. Additional functions are available using a few familiar keystrokes:

• The cursor mode or operation can be readily identified with a help label by selectingthe right mouse button. An identifier label also appears in the lower ruler of the datageometry.

❏ To select the closely related operation specified in the help label:Select ALT (or the middle mouse button).

❏ To reset this ALT operation to another related operation:Select SHIFT-CNTRL-ALT, then select another operation button (e.g. movecursor instead of delete cursor -- you will see the help change accordingly).

❏ To reset this function:Repeat the SHIFT-CNTRL-ALT combination, and select the original operationbutton.

❏ To zoom in any cursor mode:Hold down the SHIFT key.

• Select CNTRL (or right mouse) to access the popup menu from which you can selectthe Level Tool, autopositioning, etc.



CURSOR MODES

The Cursor Tool can be used in various modes (discussed briefly in the table below) toperform operations on geometries. Each mode in turn has a number of operations(described in the Delta User’s Reference: “Mouse Cursor Tool” on page 4-1.) The DataSlate is invoked here to illustrate cursor operations. It is described in its online help.

Select

Zoom (F1) To zoom in on a portion of the file by holding down themouse button and dragging over the area you wish to zoom.

Select (F2) To select the file as the current geometry by clicking on it.

Region (F3) To draw regions and obtain the coordinates of an area of thegeometry. White index marks showing the boundary of theregion will be displayed on the axis (Both axes for 2D). Theregion can be moved freely in the display area.

Cursor (F4) To use cursors to see the coordinates of a particular point inthe data file.

Note: if data areas are connected, manipulatinga cursor in one area will affect the cursor in aconnected area.

Reference (F5) To set a chemical shift reference point.

Peak (F6) To manipulate peaks and integrals, and to set their noiseand threshold levels.

Pick (F7) To measure x and y coordinates.

Integral (F8) To perform integration, set slope, offset and length forintegrals, and to manually integrate areas.

Text (F9) To annotate the file.

PiP (F10) To create and frame a selected part of the geometry withinthe present one. This picture within a picture is linked tothe original geometry.

Offset (F11) To offset the data display in data overlay.

Molecule (F12) To import standard molecule files (*.mol) into a Deltadata file to display a molecular representation of the datawith the spectrum in the geometry widget. This mode (inconjunction with add-select peak operations) lets you selectatoms within molecules and link them to peaks.

Cursor Modes


Zoom, Region, PiP -- a SamplerThree modes -- Zoom, Region, and Pip -- allow you to isolate a segment of the data forcloser study.

ZoomUse zoom operations to isolate a segment of a region for closer study.

❏ To zoom in on the data:• Select Zoom mode in the Mouse Cursor Tool:

Select . Then draw a box around the area which you want to see fill the screen.

Figure 5-15. Sample Zoom Operation Note: This zoom button in the mouse cursor tool also works in 1D and nD

Processors.



RegionUse region operations to create, move, resize or delete a geometry region.

❏ To create a region:

Select and draw the region. White index marks showing the boundary ofthe region will be displayed on the axes. The region can be moved freely in thedisplay area.

Note: When the mouse button is released, the associated Data Slate will beupdated. When you delete a region, the associated Data Slate window will beclosed. When you create a region on a data slate, a virtual geometry of thisregion pops up on the adjoining data slate. These two regions are connected bydefault. An operation performed on one appears on the other (e.g., if you createa cursor, it appears in the other geometry; if you zoom in on the data, the othergeometry reflects this zoom.)

Figure 5-16. Sample Region Operation

Cursor Modes


PiPPiP allows you to create a virtual sub-geometry, an “independent child” with thesame data as the parent geometry in which you can show or print expansion (forexample).

❏ To create a PiP:With the Pip mode on the cursor tool selected, select:

to zoom in on and frame a part of the geometry.

(or Prettify in the menu, or type p to moves the PiP to the upperleft of the selected geometry.

Figure 5-17. Sample PiP Operation



MENUS FOR EXTENDED 1D PROCESSING

This section discusses PostTransform (page 5-26) and Display (page 5-33) functions.

Post Transform Functions

PostTransform functions are data analysis and reduction functions applied after an FFT.Only phasing and baseline correction will be discussed here. The Delta User’s ReferenceGuide lists all of these functions (page 7-24).



Figure 5-18. Spectrum before Phase Correction.

❏ To phase a spectrum manually:Use the P0 and P1 buttons in the lower right-hand corner. The data in the outputwindow will immediately reflect the phase change.

1. Adjust P0 by clicking the appropriate button. Each click will increase the value ofP0 by the value on the button. (See Figure 5-19.) Use P0 to phase the area aroundthe pivot point (PP).

2. Adjust P1 by clicking the appropriate button. Each click will increase the value ofP1 by the value on the button. (See Figure 5-20.) The P1 correction will have thegreatest effect farthest away from PP.

To get a better look at the data peaks and baseline, and to make the phasingeasier, use the Zoom cursor to expand the spectrum, vertically andhorizontally. Zooming may be done at any time without affecting the phasing.To unzoom the data: use the Backspace key, or the Home key.

PP

PO

P1



Figure 5-19. Phase Correction Performed Using P0

Figure 5-20. Further Phase Correction Using P1



Selecting the Phasing Pivot Point (PP)Some data may be phased more easily by moving the phasing pivot point (PP). ThePP point is the data point that is not affected by the P1 phase correction. It is shownby the yellow tick mark on the x-axis. The value of PP is displayed in the box locatedbelow the P1 buttons.

❏ To change the PP:1. Select the Pick mode on the Cursor Tool (CTool) or F7.

2. Select , then click the Pick cursor on the data at the new PP location.

Storing the Phase CorrectionWhen the spectrum is satisfactorily phased, the newly adjusted phase correctionmust be inserted into the processing list because the interactive phase correction isapplied solely to the visual display (to improve display response).

❏ To apply the phase correction to the data:Select the Apply Phase option under the PostTransform - Phase submenu, thenprocess the data. You can also click the Apply button. The values from the P0 andPP input boxes will be transferred to the processing list. Be sure to select the Processbutton to apply the phase information to the data set.

Figure 5-21. Applying the Phase Correction



Automatic PhasingThe data system can also calculate approximate phase corrections for you.

❏ Invoke Autophase in one of these two ways:

1. Select from the 1D Processor icon bar to calculate the autophase correctionand place the results in the P0 and P1 boxes. You may touch up these autophasecorrections, but you must always apply the values using the Automatic Phasecommand under the PostTransform menu.

Note: Automatic Phase can also be run by selecting that command in thePostTransform - Phase menu.

2. Or, select the Automatic MachinePhase option under the PostTransform - Phasemenu. MachinePhase will be inserted into the processing list and will be executedeach time the processing list is applied to the data. Machine Phase autophases thespectrum using the experimental and machine parameters: pulse width (X90), deadtime, pre-acquisition delay, filter type and filter width. If these required parametersare not present (as in the case of older files) it defaults to the same algorithm as theone-dimensional Automatic Phase. Only the current major axis is phased.

Interactive Baseline CorrectionAfter phasing, NMR data may have an baseline that is uneven. If the BaselineCorrection - Base Correct automatic processing command under thePostTransform menu does not completely correct the baseline, you can use theInteractive Baseline Correction, Base Correct (Interactive). A separate interactiveiBase_Correct window will appear during processing (Figure 5-22). TheInteractive Baseline Correction allows you to apply a polynomial (up to 5th order)correction, a piece wise linear correction, or a trigonometric function correction.



Figure 5-22. Interactive Baseline Correction - a) Polynomial and b) Piece wise Linear

You can position up to 32 points in the data to fit any of these functions.Select:

• to create a new data point marker which will be displayed as a crosshair.Create a second cursor with the mouse.

• to delete a data point marker.

• to move the closest data point marker to a different position in the data set. If more than 32 points are required to correct the baseline, correction can be

applied successive times. In this case, select the number of neighboring datapoints averaged (Ave Pnts:), and turn on or off the automatic selection of theEnd_Points.

• Preview the fit on the display (Figure 5-23) by using the Preview button before thedata is changed (the Accept button). A dual display mode can be enabled by using theShow Curve button (Figure 5-22).

a) b)



Figure 5-23. Interactive Baseline Correction Preview

Figure 5-24. Interactive Baseline Correction with Show Curve Enabled



Display FunctionsVarious display functions in 1D processing are discussed below.

Axial UnitsThe NMR spectrum axis may be displayed in several different units. Immediatelyafter the FFT, the units will be Hertz. The units may be converted to parts per millioneither by inserting the PPM command in the processing list (Figure 5-25) or bychanging the ruler axis to PPM under the Rulers menu.

The PPM command changes the base unit of the data file. This differs from theRuler change, which is a temporary change for that window only. The next timethe data file is opened, the units will revert to the base file units.



Figure 5-25. Process list after converting data axis to PPM

ReferencingReferencing the NMR spectrum allows you to mark the chemical shift axis relativeto a known value. For NMR data collected on an Eclipse spectrometer, the data willbe automatically referenced by the spectrometer. For other JEOL NMR data such asGSX or EX, select Automatic Reference under the Display menu of the 1Dprocessor. For non-JEOL NMR data, you must use the Reference option in theDisplay menu, or the Reference Tool under the Delta Console.

Referencing Eclipse NMR DataNMR data from an Eclipse NMR spectrometer will already be referenced based onan absolute frequency from the gamma.def and solvent.def file. If thereference needs to be adjusted, use either the Reference command in the Displaymenu or the Reference Tool. You can also use the Reference - Unreference setting.

Reference ToolThe Reference Tool (Figure 5-26) is located under the Tools menu in the DeltaConsole.

Figure 5-26. Reference Tool



❏ To set reference registers:1. Open the Reference Tool from the Tools - Geometry Tools menu of the Delta

Console.2. Select the Reference mode from the Cursor Tool.

3. Select . Then click on a spot in the geometry. The current referencecoordinates will be displayed in the Reference Tool. They can be rounded off to thenearest whole number by selecting Round in the key menu or by pressing R on thekeyboard.

Reference CommandThe Reference option in the Display menu of the 1D processor assigns a referencepoint to any location in the data using a processing list. The Reference function takestwo values: the position in the data and the new reference value. These values areentered into the boxes below the processing list as shown in Figure 5-27. Click theProcess button to execute the processing list.

Automatic Reference CommandIf the NMR data was imported from a JEOL GSX, or EX spectrometer, theAutomatic Reference command will calculate the 0 PPM reference position andapply it to the data. This calculation is valid only for H and C data.

Figure 5-27. Reference in Processing List

❏ To enter position and reference values in this processing list:

• Select , then to indicate the peak position.• Type in the reference value.• Process the data file.



Note: The position buffer above accepts [ppm] units.

❏ Copy Reference Tool

Figure 5-28. Copy Reference ToolThis tool (Figure 5-28) lets you finger data to copy references from a Source File to aTarget File (using the Source and Target buttons), then perform referencing on one to alldimensions of the target file. It is more fully described in the on-line help and the DeltaUser’s Reference: “Copy Reference Tool” on page 20-1.

❏ To invoke the Copy Reference tool:Under the Tools menu in the Delta console, select Geometry Tools, then Ext. Reference.Or, you may use the Reference - Copy Reference command in the Display menu.

Save CommandSelect the Save command in the Display menu to write out a data file in the processinglist, specifying a filename to save the data to. If the filename is not specified, then the filewill be saved with the same name, but with an incremented version number.

Peak Picking and Integration

❏ To adjust the peak threshold:1. To display the threshold, turn on Statistics (ALT T) in the Options menu of the pop-

up menu displayed when the right mouse button is pressed down when you are in adata geometry. In the resulting data geometry, the green line indicates the positive peakthreshold; the red, the negative peak threshold; and the gray, the noise threshold(page 5-42).

2. Place the mouse in the Peak mode from the Cursor Tool (F6).

3. Select , then drag the mouse cursor to adjust the peak threshold.4. After moving the threshold, select one of the Peak Pick & Integration icons to



execute another peak pick at the new level.

5. You also use the Peak Pick/Integrate command in the Display menu to calculatepeaks and/or integrals for the data set over a particular range. The select enumerationbox allows you to specify Peaks, Integrals, or Both.

❏ To delete a peak or group of peaks:1. Select Peak mode in the Mouse Cursor Tool.

1. Select .2. Click and drag the mouse on or across the peaks you wish to delete. The peaks should

turn yellow to indicate that they are selected.3. Press the keyboard letter “d” to delete them.

4. Or, select to delete the selected peak.

❏ To create an integral:1. Select Integral mode in the Mouse Cursor Tool.

2. Select . Place the cursor at the desired location and diagonally holding the

mouse button in the gray portion just below the x ruler. Drag to create the integral.

❏ To normalize an integral:1. Select Integral mode in the Mouse Cursor Tool.

2. Select . Then click on the desired integral. The integral will turn yellow when

selected.3. Select Set Integral Normal from the Options menu of the 1D processor.4. Enter the desired normalization constant. All of the integrals will immediately

normalize to the selected integral.

❏ To delete an integral:1. Select Integral mode in the Mouse Cursor Tool.2. Click on the desired integral. The integral will turn yellow when selected.

3. Select to delete the selected integral.

❏ To link peaks to atoms:1. Select Molecule mode in the Mouse Cursor Tool.



1. Select a peak (using ) and an atom (using ).2. Press the key corresponding to the dimension you would like to hook them up to: X, Y,

Z, A, B, C, D, E. Up to three peaks can be connected to a single atom, however, anynumber of atoms can be connected to the same peak. If an atom has already beenconnected to at least one peak, you may still connect it to more peaks but you must dothis with the Spread Sheet tool.

The following example uses the X dimension; but all dimensions work the same way.

When you connect a peak to an atom for the first time, two things happen:1. The Spin X parameter gets set and Seqn X gets set (where n is 1, 2, or 3).2. The value placed in Spin X is equal to 65536 minus the molecule window number.

Thus, for molecule window 2, 65534 will be placed in Spin X. Seqn X gets assignedthe atom number to which the peak got connected in the order 1, 2, then 3.

3. Knowing this, you can see now that a single peak cannot be connected to atoms fromdifferent molecule windows, but a peak can be connected to up to three atoms from thesame molecule window.

Figure 5-29. Spreadsheet Tool

❏ To unlink a peak from an atom:1. Select the atom you wish to detach.2. Then hold down the SHIFT key and press the key corresponding to the dimension you

wish to unhook the peak from.3. Press the T key to deselect all atoms in the selected molecule window except those that

are connected to peaks. If a molecule window is not selected, then the atoms in



window one will be deselected if it exists.You don't necessarily need to use the mouse to connect peaks to atoms. You could do theentire process in the Spread Sheet Tool (see Figure 5-29 on page 5-38.)

❏ To calculate a J coupling constant between two peaks:1. Peak pick the data.2. Select Peak mode in the Mouse Cursor Tool.

3. Select .4. Click on two peaks with the mouse button. They should turn yellow when selected.5. Press the keyboard letter “j” to calculate and display the J constant.

The coupling constant is simply the frequency difference between the peaks. Inthe case of strong coupling or second order spectra the value is not the truecoupling constant.

Peak Picking and Data ReductionPeak picking can be done either interactively using the Peak Pick & Integrationicon, or by including the Peak Pick/Integrate function from the Display menu inthe processing list. The display of the peak data and integration are controlledindependently by selecting Auto Peak Pick or Auto Integrate in the Display menu.All of the peak pick entries are also stored in the Spread Sheet.

❏ To view the peak listing on the screen:The Peak Pick viewing Option must be activated. Select Peak Pick in the datageometry popup Options menu (page 5-60) which you can select using the rightmouse button when positioned in the data geometry, or use the ALT-P acceleratorkey.

❏ TO VIEW INTEGRALS ON THE SCREEN:Activate the Integrals viewing option by selecting Integrals in the geometry popupoptions menu; or use the ALT-I accelerator key.

Automatic Peak Picking

❏ To auto peak pick the spectrum:

• Select on the 1D Processor Tool menu bar.



Figure 5-30. 1D Processor with auto-peakpicked 1H data• If a greater than desirable number of peaks are picked, select Peak mode from the

cursor tool (F6)

• Then, select to adjust the peak threshold.• Select the green threshold line and move it up to include only the desired peaks.• If you cannot see the green peak threshold line, use Alt T to turn on statistics (or select

Statistics in the Options menu that appears when you press the right cursor buttonwhen in the data geometry).

greenline



Figure 5-31. 1D Processor with adjusted peak threshold

• Then, select again. The data will now be auto peak-picked again.

Note: Both automatic Peak Picking and Integration are performed by the samefunction, although the display of the peak data and integration are controlledindependently. Integration is done either interactively using the Peak Pick &Integration icon, or by including the Peak Pick/Integrate function from theDisplay menu in the processing list. All integration values are stored in theSpreadsheet.

greenline



Pick ToolUse the Pick Tool to pick a geometry with precision.

Figure 5-32. Pick Tool

❏ To invoke this tool:Select the Pick Tool command found under Geometry Tools in the Tools menu of theDelta Console. Use the Select File button to select the file whose picks you want tocontrol, and finger its geometry. When the geometry is selected, the maximum values foreach ruler are loaded into the constrained input boxes. This tool is more fully described inthe help file (page 44-1).

Noise Level and Threshold

❏ To view the noise level and threshold:• Perform a zoom on a selected portion of the baseline of the data geometry, until you

clearly see the noise.• Turn on Statistics (ALT-T) in the popup geometry Options menu. Statistics will

show on the 1D display as three lines: positive threshold, noise level, and negativethreshold (see Figure 5-33).



Figure 5-33. Peak Pick Threshold Display

Note: The Home key on your keyboard will take you back to the original viewof the data. The End key makes the top peak move to the top of the screen.

❏ To adjust the threshold and noise level:Select Peak mode in the Cursor Tool. Then use the following Cursor tool options to adjustthe zero line, threshold, and noise levels. After the new threshold and noise level is set,click the Peak Pick & Integration icon to execute a new peak pick.

Select:

To set the peak threshold (green and red lines). The positiveand negative thresholds are coupled and movesymmetrically about the zero line.

Negativepeakthreshold

Noise threshold

peak thresholdPositive



❏ To manually pick peaks:Peaks may be added or removed manually using Peak mode on the Cursor Tool.

❏ To add a peak:1. Turn on peak viewing with Peak Pick (ALT-P) in the data geometry popup

options menu. If the Peak Above option (ALT-U) is not on, the lower display areawill shrink to make room for the peak value display.

2. Put the Mouse Cursor Tool in Peak mode.

3. Select .4. Click on the spot where you wish the peak to appear.

If the peak does not exceed the current threshold and noise level, a message windowwill appear. Adjust the threshold and noise level as described above to add a smallpeak.

❏ To force create a peak:1. Put the cursor in Peak mode.

2. Select . This creates a peak pick whether or not that data position meetsnormal peak criteria.

❏ To select a single peak:1. Put the cursor in Peak mode.

2. Select .

3. Click on the peak position with the mouse button. The selected peak will have asmall yellow marker.

❏ To select an additional peak:

Select .

To set a noise threshold level (gray line) to screen out thenoise for better peak selection.

To adjust the baseplane of the data display (white line).

Select:



❏ To select a whole range of peaks:Click the mouse button and drag across the desired peaks, then release. The selectedpeak values will be displayed in the cursor color.

❏ To select all peaks in a data set:Put the cursor in Peak mode, and press the keyboard letter “a”.

❏ To remove a single peak from a data set:

Select .

❏ To remove a group or range of peaks:Select the peaks with a click and drag with the mouse button. Press the “d” key todelete the selected peaks.

❏ To remove all the peaks:Select all the peaks by pressing “a”, then delete the peaks by pressing “d” on thekeyboard.

❏ To display peaks:The Peak listing will normally be displayed underneath the peaks (default) as shownin Figure 5-34. The Peak listing may be displayed above the peaks (Figure 5-35) byselecting Peak Above in the data geometry popup options menu, or ALT-U.

Figure 5-34. Peak Display (default)



Figure 5-35. Peak Display with Peaks Above Option Enabled

Coupling ConstantsCoupling Constants are a special class of the peak display type. When two peaksare selected, the difference between the peaks in Hz will be calculated by typing theletter “j” on the keyboard (Figure 5-36). The coupling constant value will also beentered into the Spreadsheet.

The calculated coupling constant is simply the frequency difference betweenthe peaks. In the case of strong coupling or second order spectra the value isnot the true coupling constant.

Figure 5-36. Peak Display with J Coupling Constants

Integrals

Use integral operations to set slope, offset and length for integrals, and to manuallyintegrate areas of a geometry. For more detail on all Integral functions, consult page 4-21.



Manual IntegrationIntegrals may be added or removed manually using the Integral mode on theCursor Tool. These operations let you set slope, offset and length for integrals, andmanually integrate areas of a geometry.

❏ To add an integral:1. To activate Integral viewing, select Integrals (ALT-I) in the geometry popup

options menu.2. Then, select Integral mode in the Cursor Tool (F8).

• With the create integral button selected, place the mouse in the ruled area of theX scale at the place where you want to begin integration, and drag it to where you wantthe integration to end.

• You can repeat this procedure for all areas of interest.

Figure 5-37. 1D processor with data peaks integrated

When an integral region is created, the slope for that integral will be computedautomatically. The software uses the average of 10 data points at each end ofthe integral region to calculate the slope correction.



❏ To select a single integral:

Select , and select an integral. Note that the selected integral turns yellow.

❏ To normalize a selected integral:• Select Options - Set Integral Normal in the menu bar of the 1D Processor. The

Integral Normal Value window comes up.

• Assign a value by typing it into the box provided. (for example, type 3 for a peak thathas three protons).

• Then click Enter. All integrals will be scaled according to that peak.

❏ To select multiple integrals:• Press the SHIFT key and click the mouse button on each additional integral.

• Use to select a group or range of integrals:Click the mouse button and drag across the desired integrals, then release the button.The selected integrals will be displayed in yellow.

❏ To select all the integrals in a data set:Select the Integration cursor mode, place the cursor in the data window, and press“a” on the keyboard. All the integrals will change color.

Integral Slope AdjustmentEach integral may be adjusted individually for slope (Figure 5-38). When an integralis selected (yellow), a blue line is displayed below the integral. This line representsthe correction function applied to that selected integral.



Figure 5-38. Integral Slope Adjustment

❏ To adjust the slope of an integral:1. Change the cursor to Integral mode.

2. Select while using the mouse to grab either end (the small box) of the blueline at the base of the integral. The slope adjustment is an up/down mouse motion.The middle mouse button will allow adjustment of the integral region length, inaddition to the slope.

❏ To remove an integral from a data set:

Select it, and then use .

Press the SHIFT key and click on the integral with the middle mouse button.

❏ To delete a group or range of integrals:Select the integrals as above and type “d”.

❏ To change the vertical gain of an integral or group of integrals:

Select the integral and type “g”. The integral will be expanded vertically to fill thescreen. The vertical gains of the data and integrals are independent; therefore, thedata may be expanded and plotted without affecting the integral gain scaling.

❏ To plot Integral Expansion:Plotting Integral Expansion allows you to view up to 12 different integrals more closely,plotting from 2 to 9 integrals on a single page. The plot lets you see each peak with itsintegral.• Select Options - Plot Integral Expansion.• This window comes up.



• Fill in the number of integrals you would like to see. The Y-scaling value, on bydefault, fits the y dimension to the plot box.

• Then select Plot to plot this data.

❏ 4.3.6 Plotting the Spectrum

• To plot the spectrum, click on in the tool bar.

Transfer Integral ToolThe Transfer Integral Tool (Figure 5-39) can be used to create, store, and retrieveintegration templates. The integral templates may be applied directly to data in otherwindows, or saved to disk for retrieval at a later time. An integration templateconsists of a list of integral and normalization regions. Normalized integrals areindicated by an “N” following the integral region in the template list.



Figure 5-39. Transfer Integral Tool

❏ To use the Transfer Integral tool:• Select Tools-Geometry Tools-Transfer Integral Tool from the Delta Console.• Select the Apply Integral command under the Display menu of the 1D Processor

to include the integration templates in a processing list.For more information on the Transfer Integral tool, see the Delta User’s Reference:“Transfer Integral Tool” on page 60-1.

Peak DeconvolutionOverlapping NMR peaks may be deconvolved to determine peak ratios. After a peakis deconvolved, the information for that peak is automatically updated in theSpreadsheet (Figure 5-49).

The deconvolution routine uses the peak positions from the Peak Pickinformation. All the peaks in the display window to be deconvolved must havepeak pick positions.



Figure 5-40. Data before Deconvolution.

Figure 5-41. Deconvolved Data



❏ To deconvolve a peak or group of peaks:

1. Peak Pick the data set and expand the desired area as in Figure 5-40.

The deconvolution will occur to all peaks in the display window. If the entiredata set is displayed, the entire data set will be deconvolved (this may take along time).

2. Select Deconvolve (ALT K) in the Options popup menu accessible from the datageometry window. This option enables the deconvolution display.

3. Select the Peak mode from the Cursor Tool (F6).4. Select the peaks to be deconvolved.5. From the Key menu, with the mouse button, select Fit Lorentzian, Fit Gaussian,

or Fit Mixed. Or, press the keyboard letters “l” for Lorentzian, “f” for Gaussian,or “x” for Mixed. Deconvolution will begin immediately.

6. Deconvolution is an iterative procedure. A chi-square value of the fit isdisplayed in the Delta Console window. Results are only displayed ifshow_deconvolution_results is true in the Preferences Tool.

7. Repeat the fit until a consistent value is obtained. The deconvolved peaks aredisplayed in yellow. The difference between the deconvolved peaks and thespectrum is displayed in red above the data (Figure 5-41).

8. The sum of the deconvolved peaks can be displayed (Figure 5-42) by usingDeconvolve Sum (ALT H) in the geometry popup menu in the Menu bar. Forexample, if you select a group of peaks, then turn on Deconvolve and DeconvolveSum,

•the green line represents the data, with its peaks.•the yellow line shows a mathematical model of each peak, called adeconvolution.•the red line above shows the difference between the actual peak and thetheoretical model -- the deconvolve sum.

9. Deconvolve Unsel will show the deconvolutions of all peaks whether selected ornot (Figure 5-43).

10. Often it is necessary to add additional peaks. This may be done at any time byusing the create peak option with the CTRL - middle mouse button feature.

11. Finally, after deconvolution, with the deconvolve bit set to TRUE, data will beupdated for the deconvolved peaks.



Figure 5-42. Deconvolved Data with Deconvolve Sum

Figure 5-43. Deconvolved Data with Deconvolve Unsel



Figure 5-44. Spreadsheet after a Deconvolution

AnnotationDELTA supports on-screen annotation, which is created with the Text mode (F9)from the Cursor Tool. The data set must be saved after the annotations are created.The annotations are stored with the data. The annotation display is controlled by theAnnotation options (ALT A) under the data geometry popup options menu.

❏ To create an annotation:

1. Locate and expand the peak of interest.2. Place the mouse pointer in the Text mode.

3. Select . The cursor will change to an I-beam insertion marker.4. Select the desired location with the marker, and press the mouse button.5. Type the text. Greek characters are accessible using the ALT key. Annotations are

limited to a single line of text.6. Type Enter to terminate the annotation input mode.

Note: When an annotation is selected (yellow), all other annotations willdisappear from the screen until the selected annotation is terminated or de-selected.

❏ To edit an existing annotation:

1. Place the mouse pointer in Text mode.

2. Select .3. Select the annotation you want to edit. It will turn yellow. Use the arrow keys to

move the I-beam insertion point to edit the string.4. Type Enter to terminate the editing mode.



❏ To delete an annotation:

1. Select2. Then click on the annotation you want to remove.

❏ To rotate an annotation:1. Place the mouse pointer in Text mode.

2. Select .3. Select the annotation; it will turn yellow.4. Press the Page Up keyboard key to rotate 90˚ right (up) or Page Down keyboard

key to rotate -90˚ left (down).Annotations may be rotated and shifted (anchored) about the insertion point.Rotation and shifts may be done at any time in any order.

❏ To shift an annotation:1. Place the mouse pointer in Text mode.

2. Select .3. Select the annotation; it will turn yellow.4. Press the Home keyboard key to shift the annotation to the right, or the End

keyboard key to shift it to the left.

Figure 5-45. Annotation Rotation & Shift KeysGreek characters can be generated by holding the left ALT key and typing in theappropriate key (a= alpha, b = beta, etc.)

❏ To change the font/attributes/size of annotations:1. Place the mouse pointer in Text mode.

2. Select .3. Then select the annotation.4. Then use the mouse cursor to bring up a selection menu.

SHIFT RIGHT

SHIFT LEFT

ROTATE 90˚

ROTATE -90˚



❏ Use these key combinations:Select:• Shift - arrow key to change the font.• Ctrl - arrow key to change the font size.• Alt - arrow key to change the font attribute.

Figure 5-46. Data after Annotation

MoleculesUse Molecule mode in the Mouse Cursor Tool to import standard molecule files (*.mol)into a Delta data file to display a molecular representation of the data with the spectrum inthe geometry widget.

Each molecule is made up of atoms and bonds. An atom is located at the both ends ofeach bond. Any number of these atoms can be selected or deselected, then hooked up topeaks in the data file using Add-Select Peak and Deselect Peak operations.

Note: Before you can add molecules to display in Delta, you must first have a.mol file that is in standard molecule file format. Delta does not yet provideany mechanism for creating these types of files, so you must create one byusing another software package. It is assumed that a.mol file exists for Deltato import.



❏ To import a molecule interactively:

Select:

To create a molecule window.ALT: To move a molecule window.

To move a molecule window.ALT: To resize a molecule window.

To resize a molecule window.ALT: To move a molecule window.

To select or deselect a molecule window. Only onemolecule window can be selected at a time per data file.ALT: To resize a molecule window.

To delete a molecule window. This will not remove themolecule information from the data file, it only removesthe window in which it is displayed.ALT: To resize a molecule window.

To select an atom. Click on the atom you wish to selector deselect. Then connect atoms to peaks in the data file,using the Add-Select Peak and Deselect Peak operationsbelow.ALT: To select peaks.

To select peaks (used to connect a selected atom with apeak in the data file).ALT: To delete peaks.

To unselect peaks.ALT: To select peaks.

Data Window Manipulations: Level Tool


• First, open a data file in a data geometry window. Any data file can have a moleculeimported into it, but only 1D and flat 2D geometries will be able to display themolecules.

• In molecule mode, select and click and drag a window on top of the

spectrum in the geometry.• A pop-up box will then appear prompting you to select a .mol file to display in the

window.• Select the file to be drawn in the window.

DATA WINDOW MANIPULATIONS: LEVEL TOOL

Figure 5-47. Level Tool -- Contour View (I) and Colors View (II)The Level Tool can be used whenever there is a data (geometry) display window on thescreen. Its effects are applied only to the currently active (selected) geometry.

Colors (II)Contours (I)



Although the main purpose of the Level Tool is for 2D contouring, it also provides amechanism for changing the colors of the contour levels and how they are drawn. You canalso use the Level Tool to turn on and off the positive and negative data. This tool isdescribed in the online help -- Delta User’s Reference Guide, page 5-1.

❏ To invoke the Level Tool:• Move the mouse inside the geometry.• Hold down the right mouse button, select Tool Configure then Level Tool. The

contour view (I, above) will display.• This tool also comes up by default when you have set the Level Tool button in the

Geometry Page of the Preference Tool.• Use the right mouse button to toggle between the two Level Tool displays.

DATA WINDOW MANIPULATIONS: GEOMETRY OPTIONS MENU

❏ Use the Options menu to perform the following operations on the datageometry:

To use these geometry options: with the right mouse button pressed, select Options inthe popup menu, then select:

All overlays [Alt O]To display the filename of all the overlays not just thecurrent one (the filenames option must also be toggledon).

Annotations [Alt A] To display text annotations added to the file.

Atom Numbers [Sh-Alt-A]

To represent the atom number as set in the .mol file.Atom numbers are displayed in the molecule on eachatom.

Atom Select Numbers[Sh-Alt-S]

Only numbers will be visible when the atom is selected.

Atom Sequence [Sh-Alt-Q]

To see the atom numbers appear above the peaks towhich they are connected. Sequence must be on (Alt-J).

Comment [Shift Alt C] To turn on the file comment.

Cursors [Alt C] To show the cursors.

Data [Alt D] To show the data.

Data Window Manipulations: Geometry Options Menu


Datapoints [Alt N]

To show data points (this marking is visible as you zoomin closely on the data).

Figure 5-48. Zoomed view of data showing Datapoints

Deconvolve [Alt K]To show the deconvolutions of selected peaks. Used for1D only. See page 3-5.




Deconvolve Sum [Alt H]To show the sum of all the displayed deconvolutions.


DeconvolveSum

Data Window Manipulations: Geometry Options Menu


Deconvolve Unsel [Sh-Alt-K]

To show the deconvolutions of all peaks whetherselected or not. Used for 1D only.

File Name [Alt F] To show the filename of the file.

Geom Zooms [Alt W] To put a blue box around the area selected for a PiP.

Grid [Alt G] To show the grid on the data geometry.

Integrals [Alt I] To display integrals.

Integral value [Alt Q] To display the numerical value of each integral.

Line Hiding [Alt L] To hide lines in stack plots.

Molecules [Sh-Alt-M] To show/hide the molecule windows.

Molecule Border [Sh-Alt-D]

To turn on/off the border around the molecule windows.

Molecule Titles [Sh-Alt-T]

To show/hide the title(s) in the molecule window.

Negative Levels [Sh-Alt-N]

To show/hide negative nD data levels (hides them whenoff).

Peak above [Alt U]To display peak position above the peaks in 1D datageometries.

Peak Integration [Alt E]To display the integral value of the peaks in 1D datageometries.




DATA INFORMATION DISPLAY: SPREADSHEET TOOL

The Spreadsheet Tool is used to display and print peak, integral and assignmentinformation.

❏ To start the spreadsheet:

Select on the Delta Console.A red outline of a window will appear. Position the window at a convenient location, thenclick and drag the mouse to enlarge the window to a convenient size (see Figure 5-49.)

Peak picks [Alt P] To display the peak pick information.

Perspective [Alt V] To turn on/off foreshortening for 3D displays.

PiP border [Alt S] To put a blue box around PiPs.

Plot border [Sh-Alt B] To put a box around PiPs in a printed plot.

Positive Levels [Sh-AltP]

To toggle on/off the positive levels in nD datageometries.

Region [Alt R] To display regions using a white box.

Sequence [Alt J]

To view the sequential sequence assignment of aspectrum, a series of connecting marks indicatingsequence direction (e.g., these are especially helpful inassigning the 2D NMR spectra of Proteins.)

Shadow dimensions [AltB]

If the file is a slice out of a higher dimensionality file,then this displays the filename of the original file and theposition of the slice.

Show cursor tool [ShiftAlt S]

To allow the cursor tool to display on the geometry.

Statistics [Alt T]To display baseline, noise level and peak thresholds onthe geometry. See (page 3-6).

x ruler [Alt X] To display the x ruler.

y ruler [Alt Y] To display the y ruler.

z ruler [Alt Z] To display the z ruler in multidimensional files.


Data Information Display: Spreadsheet Tool


Loading Data into the Spread Sheet

❏ To load the Spread Sheet with a data set:

Select on the Spread Sheet.Click on a data set in any window and the peak information will automatically loadinto the Spread Sheet. If the data set has not been Peak Picked, no information willbe displayed. For more information on the Spread Sheet Tool, refer to the DeltaUser’s Reference: “Spreadsheet Tool” on page 57-1.

Figure 5-49. Spreadsheet Tool

Drag and DropDrag and Drop lets you copy parameters from a data geometry to a spreadsheet, or fromone spreadsheet to another.

❏ Use the Drag and Drop Dragon to copy data from a data geometry to aspreadsheet:Select the right mouse cursor button (or Ctrl-left mouse button) while on a data geometry(or a spreadsheet) and, before the drag and drop dragon disappears, move the cursor to anempty spreadsheet (or other widget) and let go of the button. The values of the data willappear in the spreadsheet (or other widget).

❏ Use Drag and Drop to copy, from one window to another:• text• data parameters -- from a geometry into a spreadsheet or from one spreadsheet to

another. For example, Drag and Drop lets you transfer information about peakintensity (height on the y scale) and integrals (total area covered by a peak.)

• colors -- in the Preferences Tool only.For a fuller description of Drag and Drop, see page 3-7 and page 57-2.



❏ SAVING PROCESSED DATA

This section describes how to save 1D NMR data on the hard disk after data processing iscomplete.

To save data to hard disk:

• Click on the data save icon on the 1D Processor tool bar .The processed data is saved.

Note: The FID is automatically saved.

To save data under a new filename:

1. Move the mouse pointer to File in the menu bar in the 1D Processor window.

2. Press and hold down the mouse button.


1. Move the mouse pointer to File in the menu bar in the 1D Processor window.

2. Press and hold down the mouse button.


3. Move the mouse pointer to Save As in the pull-down menu, and release the mousebutton.

Plotting Data


The Save Data File window opens:

Figure 5-50. Save Data File Window

4. Click on .

5. Specify the filename, and click on the Ok button.

The file is stored on the hard disk, and the Save Data File window automatically closes. Note: The file version number does not implicitly differentiate between FID

data and processed data. That is, the data of version 1 is not always FID. Thefile info field will have [s] in it if it is a FID; [ppm] or [Hz] if it is a processeddata set.

PLOTTING DATA

Delta supports output only in postscript (either in color or in black & white).

❏ To generate routine data plots:

Select from the Delta tool you are in. Selecting this button brings up the PrintOptions Tool which allows you to select a data destination (printer and/or file), a printer,printer specification, paper size and orientation:

Input filefilter

File versionnumber

Currentdirectoryname


File

Typefilename

List of files



Figure 5-51. Print Options Window

Delta uses WYSIWYG (what you see is what you get) plotting. If a spectrum oroption (integral, peak pick, coupling constant, etc.) is displayed in the window, itwill appear in the plot. The default plot will cover the full page of the default plotter.The default plot device and plot format is specified in the .delta_configurefile. Consult Appendix E for more information about the .delta_configurefile.

❏ To place a standard list of parameters on a plot:Use Plot Params located under the Preference menu on the Menu bar.The default list of parameters is created by the .delta_parameter_list filein your home directory. The default plot format and parameter location isdetermined in the .delta_configure file.

❏ To customize plots, use the Presentation Manager.This powerful tool allows you to do far more than design the contents andcomposition of your printout. It is outlined below, and described more fully in onlinehelp or the Delta User’s Reference: “Presentation Manager” on page 46-1.

Presentation Manager


PRESENTATION MANAGER

.

Figure 5-52. Presentation ManagerUse the Presentation Manager to conveniently submit data to a number of processes, anddesign a meaningful presentation. For example, you could start with a single data file anddo any of the following:• create templates, page 5-70,• output the data (and/or imported text and graphics) to Presentation Manager boxes,

page 5-72,• take projections or views of the data, page 5-72,• add parameter lists, page 5-72,• organize a coherent presentation, creating links and setting limits, page 5-72, and• preview and plot the presentation, page 5-76.The Presentation Manager lets you import, process and compare data taken from



experiments run on different samples. As you become an experienced user, it will serveyou as a powerful mini processor. Judicious use of this tool -- limited only by yourimagination -- could even render obsolete use of other processing tools for certain data.For instance, you could use the Presentation Manager to print a 2d contour diagram, with a1d projection: annotating, picking, labelling or filtering its peaks.

❏ To invoke the Presentation Manager:

• Select from the Delta Console.• Or select File, then Presentation Manager (or Tools, then Presentation Manager)

from the Delta Console menu. Then from the list of files in Open Data window, makea selection and select OK.

The Presentation Manager consists of:• a number of menus and icons,• a presentation screen you use like a blackboard to design your presentation (drawing

boxes filled with data or parameter lists from geometries),• a series of rules by means of which you locate your boxes on the presentation screen -

- boxes which can include data, data parameters, encapsulated postscript (.eps), IRISimage (.rgb) or text (.txt) files, and

• four select buttons to do the following:

to get features from the fingered geometries

to get ruler limits from the fingered geometries

to disallow box movement, and

to retain the ruler settings. When off, changing a box's type will erase thatbox's rulers.

Note: Presentation manager never retains a data source, but it does the processing,making a virtual copy of any file loaded into it.

Presentation Manager TemplatesYou read data into a Presentation Manager template -- one that is predefined or one thatyou design. It is recommended that you start with predefined templates.

❏ To use a predefined template:1. Select the Template menu in the Geometry menu of the Presentation Manager menu bar.2. Select an appropriate template (e.g., cosy)

3. Select a file from the Open File window , or use to finger data from an



open geometry.

Note: The persistent rulers button on the Presentation Manager must be selected,in order to finger data into Presentation Manager.

4. If the geometry you select is a zoom view, use to select the whole file.

5. Use to load the data parameters instead.

The second option - redefining a template (then renaming and saving it) - lets you add toyour collection of predefined templates. In this manner you could add a processing list to aselected Presentation Manager box.

❏ To redefine a template:1. Select a predefined template from the selection in the Template menu under

Geometry.2. Follow the instructions below to alter:• the presentation structure (moving, deleting, creating boxes)• the linking structure, limits, and Y-scale values.3. Use the icons and menus to load and process data, and to tailor and print the

presentation.4. Save the redefined template in order to reuse it.

Once you have mastered the art of redefining templates, it is one simple step further tocreate your own templates from scratch (templates you can save to reuse as predefinedtemplates).

❏ To create a template:1. Create the presentation structure using boxes, links and limits as described below.2. Load data into this structure.

Note: In the Geometry menu, under Features, there are toggle buttons forassigning various features to selected data. Each one has a default (for instance,peak picking is on by default, though it is not always desirable.)

3. Preview the Presentation. Edit it if necessary. Save the new template to reuse it later.4. Print the Presentation.



Presentation Manager BoxesBoxes in Presentation Manager represent data processes (i.e., they are more than a niceway of organizing already processed data.)

❏ To work with data or parameter boxes:• Use the middle mouse button to draw a box. This box becomes the active box, until

you click on another box, which in turn makes the second box active.• Use the mouse button to select a box.• Use the shift key plus the mouse button to resize a box, dragging the desired edge from

within the box.• Use the mouse button and drag the box to move it.• Use the shift key plus the middle mouse button to delete the box.Once you have created boxes and placed data in them, you may organize how you wantthis data to appear, setting specific rulers for each box.

❏ To set rulers:• First, move the boxes until you have the composition you want, positioning them

precisely using the four frames at the bottom of the Presentation Manager.• The numbers in the four frames indicate the distance of a selected box's four edges

from the left, bottom, right, top boundaries of the frame. The numbers can be changedby either typing them directly into the corresponding box or by using the arrows nextto that box.

Ruler Links ToolYou may also create links and post limits on different dimensions of the files by using theRuler Links tool.

LinksThe Links tool lets you create links on different dimensions of the files. Here, PresentationManager’s features are defined by the standard that x is horizontal and y is vertical.

❏ To create a projection:Rotate the data and link the x axis of one box to the y axis of another box.

❏ To invoke the Links tool:

Select from the Presentation Manager.

❏ To create links between different dimensions from different boxes:1. Select the target box in the Presentation Manager with the middle mouse button.2. Select the target ruler from the ruler/link tool.3. Then, select the source box and source ruler from which you want to link.



4. Then, click on the Add button to create the link.

Figure 5-53. Ruler Links (Links)Note: Linking only takes place when you preview or plot the data (never before).

LimitsThis button lets you set specific rulers for any box in the Presentation Manager.Using the Limits tool, you can select specific limits on your data geometry.

❏ To set a display limit on a ruler:1. Select the target box in the presentation manager with the middle mouse button.2. Select the target ruler (X or Y) using the up and down arrows.3. Then either type the lower and upper X axis limits into the limit input boxes, or use the

arrows to adjust the limits.4. After that, select Add to set the limit.



❏ To remove a link or a limit:• Select the target box and target ruler as described above.

• Highlight the item you want to remove in the display box, then select .

Note: You cannot apply a limit or create a link to the same ruler.

Figure 5-54. Ruler Limits

Y-Scale values

❏ To set Y scale values:1. Enter the number of the target box.2. Enter the number of the source box.3. Enter the Source Box X Range, either typing in the values or selecting them using the

arrows.



4. Enter the Y scale factor.5. To set the Y scale values, select Add.

Figure 5-55. Ruler Links (Y Scale)

A box may be Y-scale linked to another box. If both are geometries, the rulers in the targetbox will:• Have an X-range as specified by the Source Box X Range.• Be centered around the y-position of the baseline from the Source Box.• Be scaled (regardless of box sizes) according to the Y Scale factor.



Previewing the PresentationOnce you have composed your “data design” you may preview how the data will lookbefore sending it to the printer.

❏ To preview a presentation, select .A sample preview follows:

Figure 5-56. Presentation Manager (Preview)

Printing the PresentationThen you are ready to print the data.

❏ To print a presentation, select .

Note: When a box is set as a box link, and IMPORT/TEXT is selected fromthe menu, the box's type is changed to TEXT_LINK. At the time of plot or display,it finds a file which begins with the filename from the source box, and ends in .txt.For example, if box2 is linked to box1, and box1 has the value: File: EX.2.

Presentation Manager Menus


box2 will attempt to open and plot the text file EX.2.txt from the user'sconfigured REPORT_OUTPUT subdirectory.

This is useful for plotting automatically generated statistical information for geometries.

PRESENTATION MANAGER MENUS

(Study these menus in the help on this tool, page 46-11).

PRESENTATION MANAGER TOOL BAR

The Tool Bar offers quick access to some commonly used functions in PresentationManager. (For a description of its icons, see help on this tool (page 46-16).



SIMPLE MODE 1D PROCESSING

If you prefer to use the Simple Mode, toggle off the extended switch in the 1D processorPreferences menu. Once your data is loaded, a 1D Processor window is displayed asshown in Figure 5-57.

Figure 5-57. Simple Mode 1D Processor

Apodization Function Commands

Dat

a pr

oces

sing

are

aF

ID d

ispl

ay a

rea

Processing C

omm

ands

Data Source Radio Toggle Buttons

Simple Mode 1D Processing


Simple Mode Processor ButtonsThe commands (buttons) for the Simple Mode 1D Processor are described in Table 5-6.

Select:

One of these four apodization functions.If no apodization is desired, useExponential with 0 Hz.

To execute fast Fourier transform (FFT) toconvert the data from a time to afrequency domain, transforming it toproduce an NMR spectrum. The FFTmust be executed before any of the lowerbuttons will operate.

To execute an autophase calculation anddisplay the result in the Phase control panelin the lower right hand corner. You maythen fine-tune the phase control if desired.

To apply an automatic polynomial baselinecorrection.

To perform an automatic reference on thedata set.

To calculate and display the peaks. Thedisplay above or below the peaks may becontrolled by turning on or off the PeaksAbove in the submenu of the popup menudisplayed when the right mouse is pressedon a geometry.

To calculate and display the integration.



To send a plot in the default format to thedefault printer.The default values are set in the.delta_configure file or by usingthe Preference Tool. To add parametersto the default plot: select Plot Params inthe Mode menu on the Menu bar.

Select:


CHAPTER 6: USING DATA SLATE

Figure 6-1. Data Slate

Data Slate (Figure 6-1) is an all-purpose data display and analysis tool that can accept 1,2, 3 or 4 dimensional data. Data Slate lets you easily overlap and connect data forcomparison, analysis, and plotting. For most routine NMR work, 1D and nD processorsmay suffice. But as you get to know DELTA, you will find the Data Slate Tool addsdimension, depth and ease to your analyses. This chapter will cover only the basic featuresof Data Slate:• opening a data slate: (page 6-2)• loading data (page 6-2)• loading multiple data files (page 6-3)• overlaying multiple data views (page 6-5)• peak picking, data reduction and integration (page 6-14)• peak deconvolution (page 6-14)• annotation (page 6-14)• advanced data slate operations (page 6-15)

More information is provided in on line help for this tool (or see page 22-1).Note: Data Slate also forms the basis of the 2D, 3D, and 4D viewer tools, andthe 3D-Slicer. Those tools, and the TSC (tubeless sample changer viewer) Tool

Chapter 6: Using Data Slate


procedures are all discussed in the online help (Delta User’s ReferenceGuide).

❏ To open a Data Slate:

1. First select the Data Slate icon from the Delta Console menu. The OpenData for Data Slate window will appear.

2. From the list of files in this window, make a selection and select OK. The Data Slatewill appear, with its menu bar and icon buttons.

LOADING DATA INTO THE DATA SLATE

Data Source Toggle Buttons

To the far left of the Data Slate menu bar (see Figure 6-1) there are two icon buttons, onewith a disk and one with a finger. Since one of these two buttons is always selected, theyact as a toggle to determine the source for additional data. When the disk icon is selected,data will be retrieved from a disk file. When the finger icon is selected, the data will beretrieved from another screen window.

❏ To load a Data Slate from disk:

• Click on the Open File folder icon .• Or select Open File (^O) from the File menu in the Menu bar.

❏ To load a Data Slate from an open window:If the finger icon is depressed, data can be loaded directly from another window.

• Click on .• Click the mouse button on any data displayed on the screen. The data will be loaded

into Data Slate.

❏ To Load Data Files using Drag and Drop

• Click on a file with the right mouse button. Then before the dragon disappears, clickon the desktop. This will open a Data Slate with a Data Geometry in it (page 22-1).

• To load a second file into the Data Slate, click on a Data Geometry with the rightmouse cursor button, then click on the open Data Slate.

Loading Multiple Data Files


LOADING MULTIPLE DATA FILES

One of the powerful features of Data Slate is its ability to display multiple data filessimultaneously. Currently, up to 16 separate data sets can be displayed. The data files canhave any dimension, frequency and data density. As new files are loaded, the Data Slatewill automatically tile the data to fill the space in the display area. The data source can bechanged at any time to load data into the same Data Slate window from either a disk file ora display area.

Horizontal and Vertical ViewsWhen multiple data sets are loaded, Data Slate will automatically tile the window toaccommodate them.

❏ Set the tile format either to vertical or horizontal mode under the View menu(Figures 6-2 and 6-3).

Figure 6-2. Vertical Data Slate Views



Figure 6-3. Horizontal Data Slate Views

Box Data ViewSelect the Box option under the View menu to tile all the data windows to an equal size(Figure 6-4). This option is meaningful only if there are more than two data sets loaded.

Figure 6-4. Box Data Slate View

Selecting Active Data Sets


In the Preferences Tools Page you can set the preference Data Slate: ViewOrientation to orient geometries in the Data Slate horizontal, vertical, or box.Defaults to horizontal.

SELECTING ACTIVE DATA SETS

A Data Slate can have multiple data sets inside a single window, but the Cursor andLevel Tools can adjust only one data window at a time. The active data geometry windowis called the “active” or “selected data.”

❏ To select the active data set:Put the cursor in a window and click the mouse button. The mouse pointer will turnyellow.

When working with multiple data sets inside Data Slate, always check to seethat you have the correct data set selected with the mouse and that the mousepointer has turned yellow.

❏ To remove a data set:

First select the data, then click on . The data will disappear and the other data setswill be resized to fill the entire window.

The trash can icon will not delete the data from the disk, but any changes madeto the data will not be saved.

❏ To save changes to the data set you are removing:

Select before selecting .

❏ To overlay multiple data sets:

Select . Either the Open File window or the Finger will appear, depending on

the data source selected (disk or finger).

After the file is selected, it will appear in a color which contrasts with the existing data(see Figure 6-5). Each data window in Data Slate can have up to 32 overlay data sets. Thecolors can be changed by using the Level Tool. Consult the User’s Reference Guide(page 22-6) for more information.

Overlaid data sets do not need to have the same number of data points or spectral width, orbe collected at the same magnetic field strength. The only requirement to overlay data isthat the data sets be correctly referenced.



Overlaid data is aligned using the axial unit reference values. If a data set is notreferenced properly, use the reference features in 1D Processor or theReference Tool to correct the problem.

Figure 6-5. Data Overlay

❏ To select a data set from among the overlaid data:Use the Select cursor mode. Then select a data set with the mouse in the overlaid datawindow, and select this mode:

The colored triangles in the lower left corner will change to reflect the active data set, andthe filename with all overlaps checked will show at the top of the filename list.

Note: This selection method will just step through the overlays, so use cautionif you have more than two data sets in the window.

❏ To remove a single overlaid data set:

Use the Select cursor mode to make the desired data set active; then select to

remove the data.

Data Slate Icons


❏ To remove an entire data window:

Select .

DATA SLATE ICONS

A summary of the Data Slate icons follows:

Table 6-1: Data Slate Icons

Select:

Use these three icons in determining data destination:

To load new data into the current Data Slate and re-tile thedata windows (default).

To replace with new data the currently selected datadisplayed in the current Data Slate. If multiple data files aredisplayed, the data in the selected data window will bereplaced.

To create a new data slate by loading new data into a newData Slate window that is spawned as a separate process.

For other operations on data (make sure the cursor is yellow):

To disallow loading of high resolution data into the slice orprojection geometries. This only shows up when the DataSlate is in Template mode.

To load data into Data Slate from disk.

To overlay multiple data sets.

To remove a data set, first select the data, then click theTrash can icon on the Menu bar. The data will disappearand the other data sets will be resized to fill the entirewindow.Also use this icon to remove an entire data window.



To remove a single overlaid data set:• Use the Select cursor mode to make the desired data set

active.• Then click the Erase Overlay icon to remove the data.

To save the processed version of the file to disk.

To plot the geometries that are displayed in Data Slate (orsend its plot to a file.) This window gives you 20 seconds tochange print options, e.g. to redirect a plot to a networkprinter. It automatically prints the geometry if you don’tclick OK or Cancel.

Figure 6-6. Print Options

To automatically peak pick and integrate the spectrum.Searches for all peaks in the file. This operation is theequivalent of auto analyzing the file using 0 hertz as thecosy parameter and whatever is set for the integral width.

Note: you cannot see these peaks until you turnon the peak pick information in the OptionsMenu.

To search for all peaks in the file and performs integration.


Select:

Data Slate Icons


Note: For the arrow buttons to work:

• After slicing, the specific Slice display area must be active.• After expansion, the 2D contour display area must be active. The locations of the

expansion slices are marked on the axis of the 2D data.

To step one slice backwards.

To step one slice forwards.


Select:



The File Math ToolThe File Math tool may also be used to perform math operations on one or two files, andthen place the result into a new, or existing, Data Slate.

❏ To invoke this tool:Select the File Math command found in the Tools menu of Delta Console, under Math.• The Format Label shows the format of the file math equation.• The Equation Label will remain empty until the file buttons have selected the files on

which File Math will operate.• # of Files allows you to perform math operations on either one or two files. When

math operations are done on two files, the two files are combined using a simplemathematical operator.

• Operator Enumeration (+, or - or * or /) lets you choose how you want to combineoperations on two files.

• Destination Button toggles between placing the resultant file into a new Data Slate orinto an existing Data Slate. To place the resultant file into an existing Data Slate:you must choose the Data Slate to which you want to add the file. To do this, click onthe menu bar of Data Slate with the selection finger cursor (which appears when youclick on the destination button).

Equation label

Format label

Unary enumerations

ConstantInputBoxes

Operator enumeration

Connected Objects


• Use File Buttons to select the files on which you want to perform math operations.When you click on a file button, the file button will turn red and the cursor mode willchange to the selection finger. Select a file by clicking on its geometry with theselection finger. This places the name of the file selected in the geometry inside thebutton and turns the button green. If the selection fails, the button turns blue again. Thefile button that selects file B is disabled when the number of files is set to one.Likewise, if the number of files is set to two, then the file B button is enabled.

• Use Unary Enumerations to select a unary operator that will act on the file. There isa long list of unary operations that can be performed. If you select NONE as the unary,then no unary operation will take place.

• Constant Input Boxes are used to enter constants displayed in the format label.

• Select to see the transformed data in the Resulting File window:

Figure 6-7. Resulting File Window

CONNECTED OBJECTS

The Connected Objects feature allows multiple data sets to be expanded and analyzed.The data may be in the same or different windows. The data sets do not need to have thesame number of data points, spectral width, magnetic field, or be in the same window. Theconnection is done on the axial unit reference value.

Because some connections are done on the axial units, the data must beproperly referenced. Use the reference features in 1D Processor or theReference Tool to correct alignment problems.

❏ To connect Multiple Data Sets

1. Invoke the Connection Tool by clicking on .2. Click the Select 1 button (see Figure 6-8). The cursor will change to the finger mode,

.



3. Move the cursor and click on one of the data sets. The finger mode cursor will changeand the filename on the selected data set will be displayed in place of “Select 1" on thebutton.

4. Click the Select 2 button. The cursor will change to the finger mode .

5. Move the cursor and click on a second data set. The filename of the second data setwill be displayed in place of “Select 2" on the button (see Figure 6-8.)

6. On the Connection Tool, the axes of the first data set are listed at the top of thecolumns; the axes of the second data set are listed below. Select the axes to beconnected. Other combinations of axes may be selected depending on the data typesor connection desired.

7. Click the Connect button to complete the connection.8. Repeat steps 1-7 to connect additional data sets.

After data sets are connected, any function applied to one of the windows should appear inthe other window(s) simultaneously. Features that can be toggled off, such as cursors,must be turned on under the Data Slate Options window to be seen. Several other featurescan be connected. See Features on the Menu Bar of the Connection Tool. For moreinformation, consult online help on this tool (page 19-1).

Figure 6-8. Connection Tool after and before a Connection is Made

Individual Data Presentation ControlAll of the data sets inside a single Data Slate window share the same display options. Thismeans that if one of the spectra has the peak picks or integration option active, then all thespectra in the same Data Slate will also have those options active.

❏ To turn display options in different data sets on or off:Use the popup menu on the Data Geometry. Move the cursor to that data geometry, thenselect the right mouse button to bring up the data geometry options window.

1st Data Set Axes

2nd

Dat

a S

et A

xes

spec_1 X connectedto spec_2 X

after before

Connected Objects


❏ TO PERFORM OPERATIONS ON THE DATA GEOMETRY USING OPTIONS: Note: Data geometry Options are quite often used in conjunction with the

Mouse Cursor Tool.

❏ Use the Options menu to perform all operations on data geometries that youcan perform in Delta processors (see page 5-60):

Panning, Rotating and Expanding DataThe Geometry Tool can also be used to pan, rotate, and expand the data in a geometry.

Figure 6-9. Geometry Tool

❏ To invoke the Geom tool:Select the Geom Tool command found in the Tools - Geometry Tool menu of the DeltaConsole.

Select:Select Geometry to work on a geometry with the tool. When you click on thisbutton, the cursor mode changes to the selection finger. Clicking on the geometrywith the selection finger will connect the geometry to the tool.



Speed Enumeration is used to control the precision and speed of the GeometryTool. The higher the number, the faster the tool will work. However, the higher thespeed, the larger the jump for panning, rotating, and expanding.

PEAK PICKING, DATA REDUCTION AND INTEGRATION

When data is loaded into the Data Slate, all the information is loaded with it. If a data sethas been previously peak picked or integrated in a 1D Processor, for example, and thedata is loaded into the Data Slate, the peaks and integrals can be displayed simply byturning on the corresponding option.

In the Data Slate, peak picking and integration (either automatic or manual) are doneidentically to the methods used in the 1D Processor. Please refer to Chapter 5.

Peak DeconvolutionWhen data is loaded into the Data Slate, all the peak deconvolution information is loadedwith it. If a data set has been previously deconvolved in a 1D Processor, for example, andthe data loaded into the Data Slate, the deconvolution can be displayed simply by turningon the corresponding option.

In the Data Slate, peak deconvolution is done using methods identical to those used in the1D Processor. Please refer to Chapter 5, page 5-51.

ANNOTATION

Annotations are also kept with stored data. Annotations in the data set can be displayedsimply by turning on the corresponding option.

In the Data Slate, Annotation is done using methods identical to those in the 1D Processor.Please refer to Chapter 5, page 5-55.

SPREADSHEET TOOL

The Spreadsheet Tool is used to display and print peak, integral and assignmentinformation. In the Data Slate, the Spreadsheet Tool functions the same as in the 1DProcessor. Please refer to Chapter 5, page 5-64.

PLOTTING DATA

Please refer to Chapter 5, page 5-67.

Connect Options on the View Menu


CONNECT OPTIONS ON THE VIEW MENU

These connect options simplify data analysis by applying the same functions to all opengeometries. They are all options you select under the View menu on the Data Slate.

Note: Connect X and Connect All can either be toggled, or both turned off.

ADVANCED DATA SLATE OPERATIONS

The Data Slate has two advanced presentation features: the Slicing and Expand options.These options are used with multi-dimensional data sets, either 2D, 3D, or arrayedparameters. The Project option is not active in Data Slate. It is used only in the 2D viewertool.

SlicingThe Slicing option (also available in 2D data viewer) works with the Pick cursor mode.

For example, in Pick mode when the pick cursor is positioned on a 2D data set,both an X and Y slice, if selected that way, would be loaded into the Data Slate window(Figure 6-11 shows an example where the Y slices are selected). Move the slice selectpositioning guides in the 2D contour map by holding the mouse button down. When yourelease the mouse button, the X and Y slices will be updated. Select the dimensions fromwhich the slices are picked under the Slicing menu Set Dimensions option (Figure 6-10).For example, to generate a set of specific X domain slices, select only Slice by Y.

Table 6-2: Connect Functions

Select View -

Connect X

To connect all currently open geometries in the Xdimension. With this feature active, you can zoom in onall geometries in the X dimension only, or applyfunctions like cursor and region in the X dimension only.

Connect AllTo connect all currently open geometries in alldimensions; for example, X and Y dimensions will bezoomed for all currently open geometries.

Connect FeaturesTo apply any function selected from Options menuacross the board. See page 6-13.

Connect Saved To save whatever connect options you check during asession.



After picking the slices, use the left/right arrow buttons on the Data Slate tool bar to stepback/forth by one slice increments through the 2D data. This helps you examineneighboring slices of data. The arrow buttons will work only when the specific slicedisplay area is active.

You can tell if the slice is selected by the color of the cursor when it is positioned over themap. In the default color scheme, the cursor will turn to yellow over a selected area andturn to red over areas not selected. Use the right mouse button to select an area when thePick cursor mode is enabled.

Figure 6-10. Data Slate Slicing Menu

Figure 6-11. Data Slate Slicing

Advanced Data Slate Operations


ExpansionThe Expand option in the Expansion menu takes a 2D data set and performs a multipleslicing operation, pulling out the specified number of contiguous slices (Figure 6-11).Specify the number of expansion slices by using the Expand... option (Figure 6-12). TheExpansion menu is shown in Figure 6-12. The initial starting position for the Expansion isset at the edge slice of the 2D object that you are expanding.

After the initial expansion, select these buttons on the Data Slate tool bar tostep through the expansions through the 2D data. The locations of the expansion slices aremarked on the axis of the 2D data. The 2D contour map area must be the active area forthe arrow buttons to work. You can tell if the 2D contour map is selected by the color ofthe cursor when it is positioned over the map. In the default color scheme, the cursor willturn to yellow over a selected area, and turn to red over areas not selected. Use the rightmouse button to select an area when the Pick cursor mode is enabled.

The linearize function lets you take the current view of a multidimensional file (Figure 6-14) -- from the X dimension -- and place them end to end. It operates on an nD data set tocompute (in the simple case of X and Y data) Y abundance for a given X.

Do not disturb a Data Slate while it is trying to create, refresh, or delete anExpansion display! All other DELTA windows will not be refreshed until theData Slate is allowed to finish.

Figure 6-12. Expand Options Menu



Figure 6-13. Data Slate Expand Display

Figure 6-14. Expand Size Selection

❏ Use the Connection Tool to connect slices or group expansion display areas(page 6-11).



INTRODUCTION

Two dimensional NMR data is processed with a specialized tool called the nD Processor.As the name nD Processor implies, the tool is designed to process and display data setsfrom 1 to 8 dimensions. This chapter will cover only basic 2D processing:

• Loading data (page 7-1)• Preparing processing lists (page 7-6)• Loading and processing 1D slices (page 7-9)• Phasing data (page 7-10)• Viewing data (page 7-13)• Contouring data (page 7-17)• Plotting data (page 7-30.)

The nD Processor displays one processing list column for each dimension. Eachdimension is treated as a separate processing list. From any dimension, the user mayexamine a 1D spectrum along that dimension with the 1D Processor.

Before using the nD Processor, the user should be familiar with the 1DProcessor and Data Slate tools. For a more detailed discussion of nDprocessing, refer to chapter 9 of the Delta User’s Reference Guide.

LOADING 2D DATA INTO THE ND PROCESSOR

❏ To invoke the nD Processor, select:

• in the Delta Console Tool Bar,• A new window to Open Data for Processing will appear (see Figure 7-1).• Browse the directories and select the two-dimensional file to be processed.



Figure 7-1. Open FileIf the nD processor is already running, or if you call nD processor from the Processorsmenu on the Delta console:

• To load new data, select .• Or, select Open (^O) under the File menu in the Menu bar.

❏ To open a new nD file and remove the current processing list, select .Processing a 2D data set begins with an empty 2D Processor.

Current Directory Name

List of Subdirectories

File Version Number

List of Files

Selected File Name of

File Info

Input File Filter

Elements of 2D Processing


Figure 7-2. Empty nD Processor

ELEMENTS OF 2D PROCESSING

DELTA software treats each axis of an NMR data set as a domain. A domain has anucleus type, spectral width, and processing parameters. An NMR data set may have onlyone major domain at a time. All other domains are called minor domains.

In order to eliminate confusion about the order of t1, t2, and t3 evolution times in NMRdata, DELTA uses the nomenclature x, y, z, α, β, γ, δ, ε to specify the domain. The xdomain is always the dimension collected by the spectrometer receiver. The y dimension isalways the next slower incrementing domain, z the next slower, and so forth.

Processing can occur only on the major domain of a data set. The Transpose commandinterchanges the major and minor domains through a cyclical rotation. For n dimensionaldata, after n applications of Transpose, the major domain will be back to the startinglocation.



The active domain is selected by the button at the top of each column. Click the button (Xor Y in Figure 7-3) to change the active domain. Only the processing list of the activedomain may be edited. If you want to partially process a data set, leave the processing listsempty (except for Transpose) for those domains you do not want to process.

The higher domains are controlled by the buttons at the bottom of the nD Processorwindow. Up to 4 domain lists can be viewed at once.

Figure 7-3. nD Processor Window

SliceConstrainedInput Boxes

ProcessingLists

Parameter

DomainControlButton

Domain Buttons

Preparing 2D Processing Lists


PREPARING 2D PROCESSING LISTS

Processing a 2D data set begins with an empty 2D Processor.1. Each domain of a 2D data set has a separate processing list. Normally, the domains are

processed from left to right; i.e., X then Y for a 2D data set.2. Each processing list column must end with the [transpose] command that changes the

major domain prior to going to the next domain.3. The [transpose] command, like the Display/Phase command in the 1D processor,

cannot be removed from the list.

2D processing lists resemble 1D processing lists (see Chapter 5). Like 1D processing lists,they may be constructed by selecting items from the Menu bar. Use the icons andcommand buttons on the nD processor for copying, composing and editing yourprocessing lists. See the discussion on the nD Processor in The Delta User’s ReferenceGuide for a detailed listing of these icons and menus.

Figure 7-4. X-Domain processing list

❏ To read a 2D processing list from disk, selectProcessing lists may be stored and recalled from disk, just as in 1D processing, usingthis icon, or the Open List option under the File menu.

X domain listselected



❏ To save a new list, or modify an existing list, select ,or the Save List option under the File menu.

You can create a new 2D processing list analogous to the way 1D processing lists arecreated, by selecting operators listed under the pull-down menus.

❏ To create a 2D processing list using the menus:1. Select a topic on the Menu Bar.2. Hold and drag the mouse to highlight the desired option or command.3. Release the mouse button and the option will appear in the processing list.You can use your first processing list as the basis for the second

Select:

To designate a disk file as source.

To designate another Processing window as source. Boththis icon and the Open File work with the Open List icon toload the Processing list.

If the processor is already running, load new data byselecting either this Open File folder icon or Open File(^O) from the File menu.

Select this Open File Clear icon or Open Clear from theFile menu to load a new file and remove the currentprocessing list.

To open a processing list from the source. If the source isset to “from disk,” the Open File Tool will appear. If thesource is set to “from another window,” the mouse pointer

will change to and the user must click on the windowcontaining the desired processing list.

To save the current processing list to disk. The Save FileTool will appear, and the user will be prompted for a filename.

To print the processing list.

Preparing 2D Processing Lists


❏ To edit a Processing List

Select:

To place the next processing item at the end of the currentlist. Even if a processing step is highlighted, the nextselected item will be placed at the end of the list.

To place the next selected processing item before theselected item in the list.

To change the selected item to the next item selected fromthe pull-down menu.

To cut the selected line from the processing list.


Note: Cut and Paste are local to the processingwindow. You can not cut and paste itemsbetween different processing windows. And you

can also use the drag and drop dragon to create a processing list:

• Select the widget from which you want to copy data.• Then, hold down the right mouse button (or select Ctrl -

left mouse button).• Before the dragon symbol disappears, move the cursor

from the selected widget to the widget into which youwant to copy the data, and let go of the button.

To erase the contents of the selected processing list.



Selecting a Data Output destinationAfter the processing list is set, select the output destination for the data using the iconbuttons to the right in the row of icon buttons (Figure 7-5). The destination may be a DiskFile, 2D Phasing Tool, Data Slate, or 2D Viewer. Clicking on the destination buttoninitiates the processing. During processing, the status is displayed in the Delta Console.

Figure 7-5. nD Process Data Destination Buttons

Delta never processes or modifies the original data. It always makes a copyfirst, then processes the copy. Therefore when large multi-dimensional datasets are processed, there may be a delay while the copy occurs. During thecopy, a message is displayed in the Delta Console.

To delete the currently selected (highlighted) item in theprocessing list. All subsequent items will be renumbered.

To copy an entire processing list from a different dimensionof the nD Processor. Select first the source domain button(e.g. X), then the Copy button, then the destination domain(e.g. Y).

Note: Each domain of a 2D processing list mustend with the transpose statement, which causesthe data to be phased and displayed in thewindow.

To start up a 1D Processor and load a 1D slice of data.

To process data and put up to 16 slices in Data Slate.

Select:

Disk FileData Slate

2D Viewer2D Phasing Tool

Loading and Processing 1D Slices


Toggling between processing list view and geometry view:

Select:If processing needs to be done, then the data will be processed when switching to thegeometry view.

Selecting Preferences

❏ TO SELECT PREFERENCES:Selecting Preferences-Plot Params Plots parameters with the file.Plot Process List Plots a processing list with a file.Plot Pop-Up When On, a printer dialog pops up when a request is sent to plot data.

LOADING AND PROCESSING 1D SLICES

Often it is desirable to look at a particular vector or 1D slice from a multi-dimensionaldata set during processing. Delta allows the user to extract any slice from the data set,process the slice as a 1D spectrum and use the 1D processing list in multi-dimensionalprocessing.

❏ To load a 1D slice of data parallel to any dimension:1. Select the column for that domain by clicking on the domain button at the top of the

processing list. The indexing value for the other domain(s) will determine whichslice is displayed.

2. Click on the 1D Slice button.3. A 1D Processor will start up and the slice will be loaded. If a processing list for that

domain already exists, it will be copied to the 1D Processor and executed.4. After the 1D Processor opens, create a processing list or make changes in an

existing list in the 1D processor as you would for 1D data.5. When the processing list is correct, select Quit under the File menu to close the 1D

Processor. The 1D Processor will close and the processing list will be transferredautomatically to the nD processing list.

6. Use the Y slice button to process data and put up to 16 slices in Data Slate.



PHASING 2D DATA

If 2D data is collected in phase-sensitive mode, it may be phased in both dimensions togive in-phase absorption mode display. Phasing is not necessary (or possible for thatmatter) in the case of absolute value or magnitude 2D data.

❏ Phasing can be done in several ways:• in the processing lists by phasing the 1D slices,• on the 2D spectrum by picking slices and processing them with the 1D Processor, or• on the 2D spectrum using the 2D Phasing Tool.The choice of the phasing method depends on the experiment and sample.

If the data has been baseline corrected or compressed by the Real command,the imaginary data has been deleted and the phase cannot be adjusted. Re-process the raw data and make the phase corrections before the baselinecorrections or before using the Real command.

2D Phasing ToolThe 2D Phasing Tool is shown in Figure 7-6. The 2D Phasing Tool allows the user tointeractively phase 2D data while observing the contours. Data may be loaded into the 2DPhasing Tool by using either the nD Processor destination buttons (see page 7-8) or

on the menu tool bar.• The first (target) file view displays the entire file.• The second (regions) view displays the phasing for characteristic portions of the file.

Note: Phase 2D will not save the phase corrections until you choose Save fromthe File menu.

Phasing 2D Data


Figure 7-6. 2D Phasing Tool

❏ To invoke the 2D phasing tool:Select the Phase 2D command found in the Processors menu of Delta Console.

Or select found in the nD Processor or the Process Tool. However, in thesecases, the data file is first processed by the tool it is in, and the result is placed in 2DPhaser.

❏ To use the 2D Phasing Tool:1. Select regions with the middle mouse button and the Region cursor tool (F3). You

may also select Region in the scroll down list for this tool. If you do so, a box willappear around each region selected.

2. Or, select and draw the region. White index marks showing the boundary ofthe region will be displayed on the axes. The region can be moved freely in the displayarea. Up to 4 regions can exist at any moment.



3. Press and the display will change to Figure 7-7.4. Use the X and Y/ P0 and P1 input boxes to adjust the contours so they are in-phase.

5. Press to apply the current phase corrections to the data. TheP0 and P1 values displayed in the input boxes will be reset to zero.

6. Use Transfer on the Menu bar to transfer the data to either a 2D Viewer or a DataSlate after phasing is completed.

For a full discussion, consult help on the 2D Phaser (page 43-1).

Figure 7-7. 2D Phasing Tool Region Display

2D Viewer Tool


2D VIEWER TOOL

Figure 7-8. 2D Viewer - Contour ModeThe 2D Viewer is a version of Data Slate specially designed for optimal display andanalysis of 2D data. 2D data is displayed as a contour map in the middle of the window.Space is reserved for projections and slices along the top and side. You can select a 1Ddata display area of the window and load a 1D file into any of the projection or slice areas(see page 7-18). The cursor turns yellow to mark an area into which data may be loaded.For more information than what is provided here, consult online help on this tool (page 8-1).

When the 2D Viewer is first started, the areas reserved for slices are displayed as theprojection data until you select the Pick Cursor and choose data slices. The 1D data labelsare always in the base units of the 2D data file. If you change the display labels with theRulers menu, the file units displayed with the slices are not affected.

❏ There are three ways to start the 2D Viewer Tool:

1. Start it directly from an nD Processor by selecting . Data is automatically

loaded after processing is completed.



2. Start it by selecting on the Delta Console. A new window called Open File

will appear (Figure 7-1 on page 7-2). From the Open File Tool, select the file to beviewed.

3. Start it from the Viewers menu in the Delta Console. When the 2D Viewer is startedfrom the Viewer’s menu, it will appear empty until data is loaded.

❏ To load new data with the Viewer already running:

Use the Open Folder icon or select File, then Open File (^O) in the menu bar.

❏ To load data in from another window to the 2D Viewer:

Use the Finger icon and select the data geometry you want to load.

Once data is loaded, you can set the level of the contour lines in the 2D Viewerwindow, if necessary (see page 7-17).

Two Dimensional Display Modes

❏ To view two dimensional data in different display modes:1. Press the right mouse button on the data window.2. From this Main Display Area menu, select the desired view.

Select:

Contour(default)

To map the 2D data as Contour lines controlled by theLevel Tool (a maximum of 24 negative and 24 positivelevels).

Mesh To map the 2D data to a wire frame surface to create a3D object. The 3D object may be rotated and zoomed.

Surface To map the 2D data to a 3D surface. The object may berotated and zoomed.

Stack To draw the 2D object as a set of 1D spectra. Thestacked object may be zoomed and panned, but notrotated or viewed from different angles. Stack modedoes allow the user to change the x and y offsetbetween slices to better see relationships betweenslices.

Image Displays the 2D data set as an intensity/brightnessmap.

2D Viewer Tool


Datadex nD To display an nD object as a series from n=1 to (n-1)Dspectra with the ability to rapidly step along the axesand move between different dimensional levels.

Select:



Figure 7-9. Mesh(a), Surface(b), Stack(c), and Image(d) Modes

(a) (b)

(c) (d)

2D Viewer Tool


2D Cursor Tool functionsThe Cursor Tool functions in 2D are identical to those used in the 1D display mode. Referto the Delta User’s Reference Guide for a fuller treatment of the “Mouse Cursor Tool” onpage 4-1.

Contouring 2D DataBecause the contours are calculated in advance, you can zoom and pan the data in real-time. Data will be automatically contoured when it is loaded into 2D Viewer, since thedefault viewing mode of 2D data is contour. If the contour levels are not satisfactory, usethe Level Tool to adjust the position and number of contours. The Level Tool allows up to24 positive and 24 negative contour levels. Individual contour levels may be turned on oroff by clicking the level buttons with the mouse.

The position of the contours is controlled by the contouring function. The contouringfunction is controlled by the Start and Bias controls. Use the mouse to drag the Start andBias control sliders. When the Start and Bias are altered, the current contour buttons willbe “grayed-out”, and the Apply button must be clicked to recalculate the display. Toimprove the interactive performance, all of the selected contours are calculated at onetime.

If the Level Tool is not already open:

• Move the mouse pointer into the 2D data display area in the 2D Viewer window.

• Then press the right mouse button to display the pop-up menu, and select Level Tool.The Level Tool window opens.



Figure 7-10. Level ToolStart sliders Determines the minimum intensity of the bias. Set these so

that the base level is positioned at the bottom of the LevelTool window.

Contour-lineButtons

Bias Box

Apply Button

buttons Plus and Minus

Baseline

Noise threshold

Peak threshold

Start Slider

s

Negative contours

Positive contours

Preset buttons

Bias Slider

2D Viewer Tool


• Adjust the number of contour levels drawn by clicking on the contour-line buttons inthe Level Tool window.

• Adjust the number of contour levels drawn by clicking on the contour-line buttons inthe Level Tool window.

The levels of the contour lines are set based on the noise level, automatically obtainedafter data processing is completed. Only the colored buttons have been computed.

Changing Contour LevelsThe levels of the contour lines are set based on the noise level, automatically obtainedafter data processing is completed. Only the colored buttons have been computed.

Often the threshold for the 2D display must be adjusted for optimum presentation or toobserve crosspeaks of lower intensity. The contour algorithm is an exponential functionand has two adjustable parameters: Start and Bias. These are displayed as sliders on theright side of the Level tool.

• Bias adjusts the spacing between adjacent levels.• Start adjusts the starting position.

Use the mouse to drag the Start and Bias controls. When Start and Bias are altered in anyway, the current contour levels are “grayed-out” and the Apply button must be clicked torecalculate the display. If you accidentally move the Start or Bias control, click on the 2Dspectrum with the Select mode cursor and the Level tool will return to the current viewStart and Bias values.

The Delta User’s Reference Guide (online help) describes the Level Tool in greaterdetail (see “Level Tool” on page 5-1).

❏ To change or compute new contours:• Click on a grey contour-line button.• Click on the Apply button in the Level Tool window.The contour lines are redrawn.

Note: If you try to draw contours too far down into the noise, a dialogue boxwill pop up informing you that it will not draw all the points asked for. This isto guard against bogging down the computer.

Selecting the appropriate settings for the Level Tool is important, as seen in the followingdemonstrative examples.

Preset buttons Sets the number of contour lines.

2,4,6,8,12, 16 and 24 may be preset.

Contour-line levelbuttons

The level can be set manually by clicking on each button tohighlight it.

Bias slider Determines the slope of intensity. If the slider is located nearthe top of its range, a lot of contour lines are drawn at the lowend of the spectrum. See below.



Figure 7-11. Data with too few (only topmost) contours selected

Figure 7-12. Data with too many contours selected (well into the noise floor)

2D Viewer Tool


Figure 7-13. Data with a sensible distribution of contours selected

• If you have calculated a contour that is too low into the noise, you can simply turn offthat level display by clicking on the appropriate Contour Level button on the LevelTool. The Contour Level button will appear to “pop up” and that selected contourlevel will immediately turn off in the display. The Contour Level button will remaincolored, indicating that level has been calculated. To view it again, simply click thesame colored button.

• Display positive and negative contour levels independently using the (+) and (-)buttons at the bottom of the Level Tool. These buttons will turn on or off all of theContour Level buttons in the associated column.

Overview AreaIn the upper right hand corner of the 2D Viewer is the Overview. This is a small windowthat always shows the entire data set. If the display has been zoomed, the zoom area isindicated by a rectangle in the Overview display. The Overview is an active data area;zooming and panning can be done from this area.

Zooming and Panning 2D DataThe mouse is used for zoom and pan control with 2D data as well as with 1D data.

❏ To use the zoom:

1. Select Zoom mode (F1) on the Cursor Tool.



2. Then select to select a rectangular area from the 2D data.3. You may also use Zoom directly on the Overview area to move the box outline, create

another zoom area, or reshape the zoom area.4. To Zoom on only one dimension of the 2D data, click and drag the mouse button in

either axial ruler area. The rectangle will be drawn over the entire 2D display betweenthe points on the axis selected by the mouse drag.

❏ To pan across the data:

1. Select Zoom cursor mode.

2. Select this operation and drag the mouse in the axial ruler area. A slider controlwill appear as a reference when you are panning.

3. After you have finished panning, the Overview area in the upper right corner of thewindow will be updated to show you the current zoom area as a small rectangleoverlaid on the entire map.

Note: You can pan the rectangle directly in the Overlay area. The Pan functionis active in the main display; the horizontal and vertical pan are selected by themouse position. An imaginary 45 degree diagonal line from the lower leftcorner separates the Pan horizontal from the Pan vertical area.

4. To return to the previous view: press the Backspace key. The zooms and pans arekept in a history list and the Backspace key moves back one level at a time.

5. To return to the full spectrum: press the Home key.

Slice and Projection Areas

When the 2D Viewer is initialized, two separate areas are reserved along each axis. Bothof these areas are initialized with the data projections. The Display option on the Menubar allows the user to turn these areas on or off independently. The area closest to the 2Ddata, called the Slice area, is updated each time a Pick is made by the mouse. The outerarea, called the Projection, is updated when a projection is done.

❏ To finger high resolution 1D data into either the slice or projection areas:

Select the menus under Display - High Res.

The high resolution data does not need to match the 2D data in data points or spectralwidth. Alignment is done by the axial reference point; therefore, the 1D and 2D data mustbe referenced to the same peak in either Hz or ppm.

2D Peak Pick and Data Reduction


Note: If the high resolution 1D data does not line up with the 2D data, checkthe spectrum reference. When the data is newly loaded into the viewer, pressthe home key once to reset all expansions. If the data reference must bechanged, use the normal procedure for either 1D or 2D data.

2D PEAK PICK AND DATA REDUCTION

❏ To peak pick and integrate (in both 2D and 1D processing), select .

❏ To view the peaks:

1. Select Peak Pick from the popup geometry menu.2. If no peaks are displayed, it is because the data doesn’t contain peak information.

Select to recalculate and refresh the display. Peaks will be displayed asoctagons with the peak width in each direction represented by a pair of crossed lines(Figure 7-14 and Figure 7-15).

3. Select peaks with in Peak mode, dragging the mouse with the mouse buttondepressed across the peaks of interest. Selected peaks will be displayed in yellow.

Figure 7-14. Peak Pick Overlay



Figure 7-15. 2D Peak Pick Display

❏ To manually add a peak:

1. In peak mode of the cursor tool, select then select the peak. If the desired

peak does not meet the threshold and noise criteria, a message is displayed. If this

happens, select to force a peak to be created.

2. Or, adjust the threshold and noise level using the Level Tool, and select the peak again.3. Hold down the right mouse button when over the data and select Statistics from the

Options menu.

❏ To manually delete a peak:

1. In Peak cursor mode, select and click on the peak.

2. Select peaks in addition to a selected peak by selecting in Peak mode, or by

clicking on individual peaks with the mouse button while depressing the SHIFT key.The selected peaks will be colored yellow.

❏ To delete this group of peaks:Type “d” on the keyboard.



Peak Grouping

Very often, in multidimensional data, the cross-peaks exhibit fine structure and the peakpick algorithm may label each peak inside the multiplet as a separate peak (Figure 7-16).However the fine structure is often unnecessary for basic 2D analysis.

Figure 7-16. 2D Peak Multiplet with Fine Structure

❏ To simplify data by grouping it:

Select individual peaks with the Peak cursor and type the letter “g” on the keyboard. Theselected peaks will be replaced by a single peak (Figure 7-17) centered at the averageposition of the selected peaks. The resulting diameter of the grouped peak indicator is thecenters of the original peak indicators; therefore, the diameter is an indication of theapparent J coupling constant.



Figure 7-17. Peak Grouping

Peak MeldingPeak melding is similar to peak grouping, but in this case the width of the new peak liesoutside the constituent peaks (Figure 7-18). The resulting diameter of the melded peakindicator is the outside limit of the original peak indicators.

Figure 7-18. Peak Melding



Integrating 2D DataThe integral features of 2D are very similar to 1D data (see Figure 7-19). Although theindividual peaks are automatically volume-integrated when a peak pick is done, the user

may create an arbitrary integral using in the Integration mode of the MouseCursor Tool. The integral limits are rectangular and the bounds are forced to the nearest

data point. Individual integrals can also be deleted by selecting .

When the integral rectangle is selected it will change to yellow. You can also hit the Deletekey to remove this integral.

Figure 7-19. 2D Integration.

Annotating 2D SpectraAnnotation is performed with the cursor Text mode. To display the annotation (Figure 7-20), the Annotation option (ALT A) must be selected in the popup geometry menu.

If the annotations do not remain displayed on the screen, check that theAnnotation option in the Options menu on the popup geometry menu isselected.



Figure 7-20. 2D Annotation

❏ To create an annotation:

1. Locate and expand the peak of interest.

2. Place the mouse pointer in the Text mode and select to type text at anylocation you select.

3. Greek characters can be created using the ALT key with the appropriate Englishletter. Annotations are limited to a single line of text.

4. Type Enter to stop annotating.

❏ To edit an existing annotation:

1. Place the mouse pointer in Text mode.2. Select the annotation with the mouse button. The annotation will turn yellow.

3. Select to edit the annotation.4. Select Enter to terminate the editing session.



Rotating and Shifting Annotations

Annotations may be rotated and shifted (anchored) about the insertion point. Therotation and shifts may be done at any time in any order.

❏ To rotate an annotation:

1. Place the mouse pointer in Text mode.2. Select the annotation; it will turn yellow.3. Press the Page Up keyboard key to rotate 90˚ right (up) or Page Down keyboard

key to rotate 90˚ left (down).

❏ To shift an annotation:

1. Place the mouse pointer in Text mode.2. Select the annotation; it will turn yellow.3. Press the Home key to right justify the annotation or the End key to left justify it.

4. Select this operation to move the text.

❏ To change annotation fonts:

Greek characters can be generated by holding the left ALT key and typing in theappropriate key (a= alpha, b = beta, etc.)You can bring up a menu to change the font/attributes/size of annotations by selecting

then selecting the text, then using the mouse cursor to bring up a selection menu.Or use these key combinations:Select:• Shift - arrow key to change the font.• Ctrl - arrow key to change the font size.• Alt - arrow key to change the font attribute.



Figure 7-21. 2D Spreadsheet

Spreadsheet ToolThe Spreadsheet Tool is used with multi-dimensional data just as it is with 1D data. Theonly difference is that there are more columns for the chemical shift and assignments(Figure 7-21). See page 57-1 for more information.

Plotting 2D Data2D data may be plotted directly from 2D Viewer using the print icon on the Menu bar.From the Printer Tool, you can select a data destination, a printer, printer specification,paper size and orientation:

Fields



The default plot orientation is specified in the .delta_configure file in the user'shome directory. The default 2D Viewer plot will include the contour data and the 1D dataor projections.


CHAPTER 8: PROCESSING RELAXATION DATA

INTRODUCTION

This chapter covers these topics:

• basic use of the T1 Analysis tool (page 8-1),• collection of relaxation data (page 8-1),• calculation of relaxation times (page 8-3), and• plotting of relaxation data (page 8-9).

NMR relaxation data is calculated using the T1 Analysis Tool.

❏ To use the T1 Analysis tool:

Select Viewers, then T1 Analyze, on the Delta Console menu bar. This tool can processT1 data (both inversion recovery and saturation recovery) and T2 data. The tool is designedto hold a two-dimensional data set, x_domain by time.

By selecting different mouse cursor modes with the Cursor Tool, the user can performdifferent operations on the data file inside the geometry.

• Use Peak mode to select peaks. The mouse cursor will be set to Peak modeautomatically when the T1 Analysis Tool is opened.

• Use Pick mode to take slices of the data for the T1 Analysis Tool.• Use Zoom mode to get a closer look at a portion of the data.

COLLECTING RELAXATION DATA

Relaxation data must be collected using arrayed parameter. Arrayed parameters allowyou to perform an experiment several times, collecting data for different values of thesame parameters set up in advance.

❏ To set arrayed parameters from any section of the Experiment Tool:

Click on a parameter label in the Experiment Tool Instrument window to bring up thetool for that parameter. Parameters can be set by either typing in the values directly or byentering:1. An array of numbers.First select the dimension, then type the numbers into the white input box. Select the uparrow to sort the values in ascending order, select the down arrow to sort the values indescending order.

Chapter 8: Processing Relaxation Data


2. A linear, logarithmic or exponential array.In these arrays, you provide the starting point, the stopping point, and the number of pointsin the array.

❏ The following experiments may be used:

Table 8-1: Relaxation Experiment

T1 inversion recovery double_pulse or double_pulse_dec

T1 saturation recovery double_pulse or double_pulse_dec

T2 cpmg

Collecting T1 Data


COLLECTING T1 DATA

Because the data set can only be collected in the x-y plane, we have to set up an array oftau values for the experiment to collect T1 data. Set up an array of tau values by using theArray Parameters tool.

PROCESSING RELAXATION DATARelaxation data should be processed using the standard the nD Processor tool to processthe x dimension. The nD Processor can be automatically loaded when the experiment isfinished by setting the experiment process function to process_ndimensional.

Use the Slice option to load the first slice from the relaxation data set to set the processingand phasing parameters.

❏ To load a 1D slice of data parallel to any dimension:

• Select the column for that domain by clicking on the domain button at the top of theprocessing list. The index value for the other domains will determine which slice isdisplayed.

• Select the 1D Slice button: .A 1D Processor will start up and the slice will be loaded. If a processing list for thatdomain already exists, it will be copied to the 1D Processor and executed. After the 1DProcessor opens, you may also create a processing list or make changes to an existing listin the 1D processor as you would for 1D data. When the processing list is correct, selectQuit under the File menu to close the 1D Processor. The 1D Processor will close and theprocessing list will be transferred automatically to the nD processing list.

Click on to process the file and save it to disc or to save the data to a DataSlate.

CALCULATING RELAXATION TIMES

❏ To start the T1 Analysis tool:

Select Viewers then T1 Analyze from the Delta Console menu bar. A new window shouldappear. It will remain empty until you load an appropriate 2D data file, at which time itwill resemble Figure 8-1.



Figure 8-1. T1 Analyze Tool

Calculating Relaxation Times


Select:

To load a data set into the T1 Analysis Tool. Depending onwhether the disk icon or the finger icon is depressed, thedata file will be opened either from disk or from ageometry. When the data has been loaded, the top windowwill display the first slice of the relaxation data set. Use thearrow buttons in the upper right corner to toggle betweenthe first and last spectrum in the data set.

To generate the peak list from the 1D data. This is normallydone on either the first or last 1D data slice in the file. Thisstep is not required to calculate a relaxation value. Adjustthe Statistics (threshold, noise level, baseline) as necessary.This peak pick process can be repeated; therefore, it is bestto start with a high threshold and work down.The peaks’ intensities and Y values should appear in the listbox in the middle of the window.If the data set contains incorrect data points, you may needto choose a peak to see values. Remove them from the fit byselecting the points in the intensity list, and clicking theDelete button. The points may be added back to the fit withthe Undelete button.

To step one slice in the file in the negative/positivedirection.

To slice a file from a place you have picked.

Note: When this toggle button is depressed, themouse cursor will change into Pick mode.Clicking the mouse anywhere within thegeometry will update the value display windowand the graph down below.



To slice a file from the nearest peak. Use search widthinput box on the upper right corner to set the range.

Note: When this button is depressed, the mousecursor will change into Peak mode. If Slice isselected, the value display window and thegraph below will be updated only by clicking ona peak. Also, when this button is pressed, thedata file must be peak picked before T1 analysiscan be performed. Select Auto Analyze underthe File menu or the peak pick icon to performthe peak picking.

To step one vector in the negative/positive direction.

To slice directly from the nearest peak.

Note: This choice is available only when the ByPeak button is depressed.

To take peaks nearest the slice point.


To take peaks nearest the previously selected peak.


Note: Slice, Track and Track Drift are radiobuttons. Only one of these buttons can be on.

To use peak height for intensity of point.

Note: Peak Height and Integral are radiobuttons. When one is on, the other is off.

Select:



❏ To calculate peak intensities and Y values:1. Select a region of interest using Zoom mode.

2. Use to select the slice desired in the data set.

3. Select either or , then choose

, , or .

4. Then position the cursor anywhere in the data to select a position for calculation.Normally you will select a peak.

Note:

• When and are pressed, selections will bemade only when you pick a peak.

• is pressed, the data file has to be peak picked first.

5. Select Auto Analyze under the File menu or to peak pick the data file.

6. The peak's intensities and Y values should appear in the list box in the middle of thewindow and be graphed below.

7. If the data set contains points which may be incorrect, you may remove them from the

fit by selecting the points in the intensity list, and clicking on .

To use peak integral for intensity of point.

Note: Integral may only be used for Track andTrack Drift, not for Slice.

Select:



8. The points may be added back to the fit with the button.

Fitting Relaxation Data

❏ To fit relaxation data:

1. First, select the desired fitting model from the Curve Fit expression window whosebuttons are outlined above.

Delete To delete the currently selected value.Undelete To restore deleted values.Log data To display the natural log of normalized data.

2. Then, select to calculate the curve fit. The data points and thecalculated curve are displayed in the lower window. The coefficients for the currentcurve, standard deviation and Chi square value are displayed in the window next to theCurve Fit Expression window.



Plotting Relaxation Data

❏ To plot relaxation data:

Select File - Plot Curve or select to bring up additional toggle buttons used forplotting relaxation data.Select:Curve & Info - To plot the fit curve with selected options.Peaks & Equations - To plot table of peaks and the fit curve equation with all thecoefficients and selected plot options.Vectors & Equations - To plot data points and equation of each vector with selectedoptions.One Slice - To plot only the current vector.All Slices - To plot all selected vectors.Curve and Params - To format a curve with parameters.Multi-Column - For information laid out in blocks.Ascii Text - Tab-delimited fields of ASCII text, useful for processing on externalspreadsheets.Vector Summary - To include the following parameters in the plot.Curve - To include a plot of the curve.Slice Point (x) - First X-value of the slice.X-value table - Table of X values of the slice.YI value table - Table of Y and I values of the slice.Curve fit equation - Equation with coefficients.Standard deviation - To include the standard deviation value of the fit curve in the plot.

Chi square (X2) - To include the Chi square value of the fit curve of the plot.Number of points - Number of data points in the slice.OK - Plot data with current state.Cancel - To cancel a plot and redisplay the data points and fit curve in the lower window.Print - to set the destination of the current file as the plotter. A toggle that lets you selectthe destination.

Note: This option is available only when Vectors & Equations and ASCII textare selected.

Save File - To invoke the Save File Tool to save the current file while plotting.

Note: This option is available only when Vectors & Equations and ASCII textare selected.

True Data - To include the true data in the plot.

Note: This option is available only when Curve & Info and Curve & Paramsare selected.



Fitted Data - To include the fitted data in the plot.

Note: This option is available only when Curve & Info and Curve & Params areselected.

File MenuSelect File -Open - To open a file from disk.Plot Curve - To plot relaxation data.Auto Analyze - To peak pick and integrate the current file.Close - To exit the tool.

Ruler MenuRuler - To select ruler type: Hertz, PPM, Percent, Points, or Seconds.



INTRODUCTION

Three dimensional NMR data, like two dimensional NMR data, is processed with the nDProcessor Tool. The nD Processor displays one processing list column for eachdimension. Each dimension is treated as a separate processing list. From any dimension,the user may examine a 1D spectrum along that dimension with a 1D Processor. Thischapter will cover only the most basic 3D processing:

• loading 3D data, page 1• elements of 3D processing, page 2• 3D Data Slate, page 8• 3D Viewer, page 8• 3D Slicer, page 12.

For a more detailed discussion of the nD Processor, refer to the DELTA User’s ReferenceGuide.

Before using the nD processor, you should become familiar with the 1DProcessor and Data Slate tools.

LOADING 3D DATA INTO THE ND PROCESSOR

❏ To invoke the nD Processor:

• Select in the Delta Console Tool Bar.

• Or select Processors, then Process nD (^N) on the Delta Console menu bar to bringup the nD Processor (Figure 9-2). Then select File - Open or

• A new window titled Open Data for Processing will appear (see Figure 9-1).



Figure 9-1. Open Data for Processing Window

• Browse the directories and select the three-dimensional file to be processed.

Note: Multidimensional NMR data sets are all processed with the NDProcessor. Each of the file's dimensions is processed separately and has its ownprocessing list. The x dimension is processed first; the y dimension next, etc.

ELEMENTS OF 3D PROCESSING

DomainsDELTA treats each axis of an NMR data set as a domain. A domain has a nucleus type,spectral width, and processing parameters. An NMR data set may have only one majordomain at a time. All other domains are called minor domains.

In order to eliminate confusion about the order of t1, t2, and t3 evolution times in NMRdata, DELTA uses the nomenclature x, y, z, α, β, γ, δ, ε to specify the domain. The xdomain is always the dimension collected by the spectrometer receiver. The y dimension isalways the next slower incrementing domain, z the next slower, and so forth.

Processing can only occur on the major domain of a data set. The Transpose commandinterchanges the major and minor domains through a cyclical rotation. For n dimensionaldata, after n applications of Transpose, the major domain will be back to the startinglocation.

Input File Filter

File VersionNumber

CurrentDirectory Name


List of Files

File Info

Name ofSelected File



Figure 9-2. Empty 3D Processor Window

Processing ListsEach domain of a multidimensional data set has a processing list (see Figure 9-2). Thesingle list is broken up into multiple domain lists for ease of usage. These processing listsare similar to 1D processing lists. Each processing list column ends with the Transposecommand that changes the major domain prior to going to the next domain. The Transposecommand, like the Display/Phase command in the 1D processor, cannot be removedfrom the list.

❏ To change the active domain:Select the active domain button at the top of each column. Only the processing listof the active domain may be edited. When the Process button is selected in theProcessor tool, the entire processing list over all domains is executed. If you want topartially process a data set, leave the processing lists empty (except for [transpose])for those domains not to be processed. Also, you may set the View to 2, 3, or 4dimensions by selecting the numbers 2, 3, or 4 at the bottom left of the window. ForFigure 9-1, the view was set to 3.



Setting the X Domain List

Each dimension of the 3D data will have a separate processing column. Normally,the domains are processed from left to right, i.e. X then Y then Z for a 3D data set.

❏ To recall processing lists from disk:

Just as in 1D or 2D processing: use the Open List option under the File menu, orselect on the Menu bar.

❏ To save a new list:

Use the Save List option under the File menu or select .

❏ To construct a 3D processing list:

The 3D processing list may be constructed by selecting items from the Menu bar aswas done for the 1D or 2D processing list.

If the selected items appear in the wrong domain, change the selected domainby clicking with the mouse on the domain title button. The depressedappearance of the button indicates that the domain is selected.

Setting the Y and Z Domain Lists

Set the Y and Z domain processing column in the same way as the X column.



Creating a Processing List

A processing list may be created either by copying from a list source, or by selectingelements for the list from the menu bar options.

❏ To process the list source and assemble the processing list for a selecteddimension:

Select:

To designate a disk file as source.

Note: Use this icon with the Open List icon toload a data set or Processing list.

To designate another Processing window as source.

Note: Use this icon with the Open List icon toload a data set or Processing list.

To load new data when the nD Processor is already open.(Alternatively, you may select File-Open File (^O) fromthe menu bar.)

To open a new nD file and remove the current processinglist.

To open a processing list from the source determined by thesource buttons.

Note: If the source is set to “from disk,” theOpen File Tool will appear. If the source is setto “from another window,” the mouse pointerwill change to and the user must click onthe window containing the desired processinglist.

To save the current processing list to disk. The Save FileTool will appear and the user will be prompted for afilename.



Building and Manipulating Processing Lists

❏ To build a processing list:

Select operators listed under the pull-down menus:1. With the mouse, select a topic on the Menu Bar.2. With the mouse button down, drag the mouse to highlight the desired option or

command.3. Release the mouse button and the option will appear in the selected processing list.

Editing a Processing List

❏ To edit a processing list:

Select:

To place the next processing item at the end of the currentprocessing list. Even if a processing step is highlighted, thenext selected item will be placed at the end.

To insert the next processing item before the currentlyselected item in the list.

To change the selected (highlighted) item to the next itemselected from the pull-down menu.

To cut the selected line from the processing list.


Note: Cut and Paste are local to the processingwindow. You cannot cut and paste itemsbetween different processing windows.

To erase the contents of the selected processing list.



Loading and Processing 1D Slices

Often, it is convenient or desirable to look at a particular vector or 1D slice from a multi-dimensional data set during processing. Delta allows the user to extract any slice from thedata set, process the slice as a 1D spectrum, and use the 1D processing list in multi-dimensional processing.

❏ To load a 1D slice of data parallel to any dimension:

• Select the column for that domain by clicking on the domain button at the top of theprocessing list. The index value for the other domains will determine which slice isdisplayed.

• Select the 1D Slice button:

A 1D Processor will start up and the slice will be loaded. If a processing list for thatdomain already exists, it will be copied to the 1D Processor and executed. After the 1DProcessor opens, you may also create a processing list or make changes to an existing listin the 1D processor as you would for 1D data. When the processing list is correct, selectQuit under the File menu to close the 1D Processor. The 1D Processor will close and theprocessing list will be transferred automatically to the nD processing list.

To delete the currently selected (highlighted) item in theprocessing list. All items following the deleted item will beautomatically renumbered.

To copy entire lists from different dimensions of the nDProcessor:

1. Select a domain by clicking on the name (i.e., Xaxis).

2. Click the Copy button.3. Select the destination domain by clicking on the

name (i.e., Y axis).

Note: Each domain of an nD processing listalways ends with the transpose statement.This statement always appears at the end of thelist and cannot be removed. Its purpose is tocause the data to be phased and displayed in thewindow.



3D DATA SLATE

❏ To start the 3D Data Slate directly from an nD Processor:

Select . Data is automatically loaded after processing is completed. You mayselect additional views in the Data Slate using the menus. Help on the Data Slate offersadditional information.

Figure 9-3. 3D Data Slate

3D VIEWER

The 3D Viewer (Figure 9-5) is based on the Data Slate. Help on the 3D viewer will giveyou additional information.

❏ To start a 3D Viewer directly from an nD Processor:

Select . Data is automatically loaded after processing is complete. The 3DViewer can also be started from the Viewers menu in the DeltaConsole. When the 3D Viewer is started from the Viewers menu, it will appear emptyuntil data is loaded.

3D Viewer


The 3D Viewer is a specialized tool for displaying 3D data. As shown in Figure 9-5, itsunique layout is designed for optimum analysis of 3D data. The 3D data is displayed as acube in the upper right quadrant of the window; the other three quadrants are reserved for2D projections. The Project menu will allow you to Toggle between 2D projections andslices (select Toggle Proj/Slice under Project in the 3D Data Viewer menu bar). Keep inmind that these are actually separate data geometries which are alternately displayed in asingle display area. Each 2D area has associated 1D projection and slice areas along thebottom. When the 3D Viewer is first started, the areas reserved for slices are displayed asthe projection data until the Pick Cursor is selected, and data slices are chosen. The 1Dand 2D data labels are always in the base units of the 3D data file. If you change thedisplay labels with the Rulers menu, the file units displayed with the slices are unaffected.

Figure 9-4. 3D Viewer Right Mouse Button Mode Selection Menus

2D Display Area 3D Display Area



Figure 9-5. 3D Viewer

Three-Dimensional Display Modes

Three-dimensional data may be viewed in several display modes. The display mode isselected by pressing the right mouse button on the data and selecting a mode from theoptions menu. Depending on the Display Area dimension, the Selection Menu will vary(see Figure 9-4). 3D Display Modes resemble 2D Display Modes.

In addition, the third dimension allows for rotation, translation, and in/out zooming whenthe Display Mode is a 3D representation.

3D Viewer


Figure 9-6. 3D Viewer - Slices

Figure 9-7. 3D Viewer - Zoomed



Loading 3D Data

❏ To start the 3D Viewer:

• Select .• A new window called “Open File” will appear (Figure 9-1 on page 9-2). From the

Open File Tool, select the file to be viewed.

If the 3D viewer is already running, new data is loaded using the Open Folder iconor the Open File (^O) located under the File menu in the Menu bar. Data can also begraphically loaded from another window into 3D viewer using the Finger icon .

3D SLICER

The 3D Slicer Tool is a specialized tool for displaying 3D data. As shown in Figure 9-8, aunique layout is designed for slice analysis of 3D data. The 3D data is displayed as a cubein the bottom right of the window and a space is reserved for 2D and 1D projections orslices. When the 3D Slicer is first started, the areas reserved for 2D and 1D are displayedas projection data.

The 3D Slicer (Figure 9-8) is also based on the Data Slate. The 3D Slicer can be startedfrom the Viewers menu in the Delta Console. When started from the Viewers menu, itwill appear empty until data is loaded. For more information, consult help on this tool.

Figure 9-8. 3D Slicer with Overlaid Spears

3D Slice Plotter


Multidimensional geometry options

3D SLICE PLOTTER

Use the Slice Plotter to plot 2D slices of 3D data files.The slices that are plotted are taken at coordinates where peaks exist in a file.

For 2- and multidimensional processing, in mesh and surface modes, thesegeometry options are added to the options menu that you call from the datageometry using the right mouse cursor:

Full Spatial Reset [Shift -Home]

To zoom out to see full data set, keeping the presentperspective.

Rotate +/- X, Y or Z[Dwn, Up, Lft, Rgt, Sh-Lft, Sh-Rgt]

To rotate the data geometry left, right or in the 3rddimension.

Translate +/- X, Y or Z[Cntl-Dwn,Up,Lft,Rgt,Sh-Up,Sh-Dwn]

To move the data set left, right, or in the 3rd dimension.



❏ To invoke the Slice Plotter:Select the 3D Slice Plotter command found in the Tools menu of the Delta Console.

❏ Select View Peaks to view a 1D projection:

❏ Select Contour Levels to set the contour levels for plotting2D slices:

❏ To select Peaks and Contour Levels:The slice you print has the same contour levels as the 3D overview geometry.Therefore, you may want to add or delete peaks and change the contour levels beforeyou begin to print slices.

❏ Select from three different orientations:

Geometry Display - Contour Levels

3D Slice Plotter


To summarize: when Slice Plotter is brought up, it calculates an XY projection (aprojection along the X and Y axes), an XZ projection, and a YZ projection. Eachprojection is peak picked, and the peaks are displayed. When the plot button is clicked on,a slice is taken from the file at the coordinate of each peak in the displayed dimension. Theslice is then queued to the default plotter.

❏ The plot selector determines the number of slices that will be plotted on onepage.

If the single page button is selected, then the plots will be queued with only one slice perpage. If the multi-page button is selected, then six slices will be plotted on each page.

❏ Finally, use the Plot Slices button to queue slices to the printer.For further information, consult the treatment of this tool in Delta online Help or in theUser’s Reference Guide.

Cursor Tool

Cursor Tool functions for 3D are similar to those used in the 1D or 2D display mode.

Start the Cursor Tool by selecting the Tab . Select a Mode by scrolling the list, thenselect an operation button. The mouse cursor will change shape based on the activeoperation.

Mode

OperationsTab



❏ Place the Cursor Tool in Zoom mode to zoom in on and rotate data.Select:

• to zoom in on the data, In either the 2D or 1D projections/slices, draw a box

around the data you would like expanded and it will be enlarged. In the 3D box youwill see a white box drawn around the data. This is not expanded but the view of it hasbeen brought nearer. To zoom out, press the backspace key to zoom out incrementally;press the home key to return to the original.

• to rotate the data around various axes. Drag the mouse horizontally to rotate

the data around the y-axis; vertically to rotate the data around the x-axis; diagonally, torotate the data around the z-axis.

• to use the crosshair Cursor. The crosshair Cursor operation differs slightly in3D displays.

• You may create and delete 3-dimensional cursors as you do in 1 and 2D,and they will be linked to the lower dimension display areas.

• You can also move this cursor in 3-dimensional space.• The crosshair button (in zoom and in cursor modes) lets you center the

crosshair in spatial or mesh mode; a 3-dimensional crosshair is placedin the display area when you click the right mouse button while holdingdown the SHIFT key. The next mouse function (move, select, orcreate) will place the appropriate cursor lines at this center mark. Thearrow keys (along with the SHIFT key) allows you to move the 3-dimensional center crosshair along any of the 3 axes.

The crosshair cursor and the pick cursor are the most usefulcursor functions in the 3D display area.

Pick Cursor• The 3D Pick position cursor in Pick mode of the Cursor tool is like the 2D version,

except that there are three intersecting planes that define the three 2D contour areas.These planes are linked to the lower dimension display areas, and the index mark onthe lower dimension axes indicates their locations. If you change the Pick cursors onthe lower dimension displays, the 3D intersecting planes will track. However, the 3-dimensional center crosshair will not be updated, so that when you select the Pickcursor in the 3D display area again all the Pick cursors will be reset to thosecoordinates. You can move the 3-dimensional center crosshair along any of the 3 axesin the Pick cursor mode.

3D Slice Plotter


❏ Use the Pick Position button to get reference values in a multidimensional datageometry:

• Move the blue crosshair cursor in the geometry and select x, y and z reference valuesby clicking on the desired position.

Note: In multidimensional geometries, select a reference point by moving thisblue cross not only up and down, left and right, but also into depth.

Note: The arrow, in multidimensional geometries, indicates the presence of apeak: red indicates negative, green positive.

Figure 9-9. 3D View Control

blue 3D crosshair

arrow



Rotating and Translating 3D Data

For 3D data, the mouse does not have the axes of freedom to adequately describe 3Dmotion. The arrow keys together with the Shift and Control keys give the necessaryadditional rotation and translation functions. The optional Spaceball, however, allows for6 axes of freedom and can be used to manipulate 3D data.

❏ To rotate or translate data using keyboard keys:

• To rotate the 3D image along the vertical axis (-X or +X), you can use the Left orRight arrow keys.

• To rotate the 3D image along the horizontal axis (+Y or -Y), you can use the Up orDown arrow keys.

• To rotate along the axis perpendicular to the display (-Z or +Z), you can use SHIFTLeft or Right arrow keys.

• The SHIFT Up arrow will translate the image back along the Z axis (into the plane ofthe screen).

• The SHIFT Down arrow will move the image out along the Z axis (out from the planeof the screen).

• The CTRL Left or Right arrow keys will translate the image left or right along the Xaxis, while the CTRL Up or Down arrow keys will translate the image verticallyalong the Y axis.

• Home will reset the 3D spatial view.

Slice and Projection Areas

When 3D viewer is initialized, three separate areas are reserved for each axis. All of theseareas are initialized with 2D data projections. The Display option on the Menu bar allowsthe user to turn these areas on or off independently. The area closest to the 3D data iscalled the Slice area and is updated each time a Pick is made by the mouse. The outerarea, called the Projection, is updated when a projection is done.


Analogous to 2D processing, 3D data peak picking and integration are performed with thePeak cursor.

❏ To view peaks:

Select Peak Pick in the geometry pop up menu. If the peaks do not match the data, it isbecause you have not selected the Peak Pick icon first. Simply hit the Peak Pick icon torecalculate and refresh the display. The peaks will be displayed as octagons with the peakwidth in each direction represented by a pair of crossed lines.


CHAPTER 10: EXPERIMENT TOOL AND ECLIPSE

EXPERIMENT PROGRAMMING

INTRODUCTION

This chapter describes the Eclipse Experiment programming language and spectrometerfeatures, offering details on:

• loading experiments, page 10-2• syntax and operators, page 10-7• the Header section, page 10-17• the Instrument section, page 10-23• the Acquisition section, page 10-26• the Pulse section, page 10-29• submitting experiments, page 10-32.• arrayed parameters, page 10-48

This chapter is intended for the NMR system manager and advanced NMR operators whoneed to customize or write experiments for the Eclipse NMR. The reader should befamiliar with the operation of the Eclipse NMR and a UNIX file editor.

This manual describes certain features and options of the spectrometer that,when used incorrectly, could damage certain NMR probes. You are urged toread and understand all of the material before making modifications to anyexperiments. If you have any doubts about making changes to an experiment,please contact either the JEOL NMR Applications department or the JEOLNMR Service department before making the modifications.

DEFINITION

The Eclipse NMR spectrometers use the concept of an experiment to control thespectrometer.

❏ An experiment contains:

Header parameters - filename, identification code, sample tracking code, operatorcomments, post-acquisition processing, etc.Instrument parameters - physical hardware control parameters, i.e., temperature,receiver gain, audio filters, etc.Acquisition conditions - NMR frequencies and offsets, data points, scans, etc.Pulse sequence - pulse widths and associated timing parameters.

Chapter 10: Experiment Tool and Eclipse Experiment Programming


An experiment contains all of the information needed to create an NMR data set. Theexperiment is also stored inside the Eclipse data set and may be retrieved from an Eclipsedata set using the Experiment Tool, the loading and running of which is described in thischapter, in online help on the Experiment tool, and in the Delta Tutorial (page 4-1). Theexperiment pulse sequence and default spectrometer parameters begin as ASCII files inthe user's experiment subdirectory or the global experiment directory. The Eclipseexperiments are organized in a local user subdirectory ~/delta/experiment and aglobal experiment directory /usr/delta/global/experiment.

Pulse Sequences

Experiments are used to generate pulse sequences. The advantage of storing theparameters with the pulse sequence is that reasonable default values for the experiment arealways set.

Parameter Files

Experiments are also used as parameter files. The default values in an experiment canfunction as a parameter set; if desired, the user may be kept from changing the defaults.

LOADING EXPERIMENTS

Spectrometer Control Tool

The Spectrometer Control Tool is shown in Figure 10-1. To load an experiment, theSpectrometer Control must have a connection to or be monitoring an Eclipse spectrometer.

❏ To load an experiment:

1. Select the Spectrometer Control Tool icon . The spectrometer control tool willappear (Figure 10-1).

2. Connect to an active spectrometer. The spectrometer uploads the spectrometerhardware parameters, parameter ranges and standard values to Delta. The experimenttool uses this information to set up experiments.

Loading Experiments


Figure 10-1. Spectrometer Control Tool after Connection

3. Then select the Expmnt button from the row at the bottom of this window to activatethe Experiment Tool. When the Expmnt button is clicked, the standard Open Filewindow will appear (Figure 10-2).



Figure 10-2. Open Experiment File Tool

See “Open Data Tool” on page 37-1 for further information on this tool.

4. Select the desired experiment from the list of files in either the 'home' (local)experiment directory, or the 'global' (system) experiment directory. The defaultlocations for these directories are specified in the .delta_configure file.

Note: A new experiment can also be loaded into an existing experimentwindow.

Experiment Tool


EXPERIMENT TOOL

The Experiment Tool is shown in Figure 10-3.

Figure 10-3. Experiment Tool

Loading Experiments from Other Data SetsThe Experiment Tool has the following icons and buttons. Their use is described here:

Table 10-1: Experiment Tool Icons

Select:

To move to different locations in the experiment window.



Submit To submit the experiment to the queue.

To select a file and apply the X dimension features fromthe file you selected. This sets the sweep width and offsetfor the domain. The focus is determined by the Sourceicon status and from either another data file (disk) oranother geometry window (finger).

To select a file and apply the Y dimension features fromthe file you selected.

To select a file and apply the Z dimension features fromthe file you selected.

Experiment Source Icons

To designate an experiment text file (default) as datasource. When the open file icon is selected, an Open Filewindow appears.

To designate a geometry or data window as the source ofan experiment. Because the experiment is stored with thedata, the experiment may be recovered from anotherdisplayed data set using this mode.

To designate a data file on disk as the source of anexperiment. Because the experiment is stored with thedata, the experiment may be recovered from a data fileusing this mode.

Open File Icons

To open a new experiment into the existing experimentwindow. All experiment parameters are initialized to thevalues of the new experiment.

To open a new experiment into the existing experimentwindow. Any experiment parameters with the same namekeep their current values.

Save Experiment Icon


Syntax and Operators


SYNTAX AND OPERATORS

The experiment file is an ASCII file interpreted by the Eclipse Experiment Tool. TheDelta program constructs the experiment window as the experiment is loaded. Control ofall experiment parameters and their initial values are determined by the syntax inside theexperiment file.

Experiments are interpreted as programs, and as such the syntax of the ASCII file must befollowed. The following general rules apply to all experiments.

Syntax Rules

• Each command must be terminated with a semi-colon “;”• The double dash “--” indicates the beginning of a comment string. All characters

after the “--” are ignored.• The Pulse section of the experiment must have a begin statement.

To save the current experiment to disk. The Save Filewindow will appear and a file name may be entered. Theexperiment file is an ASCII file interpreted by the EclipseExperiment Tool. However, any include files or macrosare expanded. Therefore, the text of the saved experimentmay look different from the starting experiment.

Match Icon

To copy the parameter values from another experimentand place them in the current window. It compares onlythe names and values of the parameters, not the pulsesequence. It will not add new parameters to the currentexperiment - only update matching parameters.

Help Icons

To bring up on-line help on the current experiment, if it isavailable.

To bring up on-line help for the experiment tool.




Operators

Addition (+)Performs addition of the operands.

Subtraction (-)Performs subtraction of the operands.

Multiplication (*)Performs multiplication of the operands.

Division (/)Performs division of the operands.

Concatenate (||)Combines or concatenates two or more sets.For example:

a = {0,0,180,180};b = {90,90,270,270};

phase_1 = a||b;-- phase_1 is {0,0,180,180,90,90,270,270}

RoundRounds the input value to the nearest integer. The input may be a variable orexpression.

Assignment (=)The assignment statement is used to equate and initialize variables and parameters.Statements using the = symbol are not displayed in the Experiment Tool, and thustheir values are not user observable or modifiable.The = symbol is also used as a Boolean operator in if-then-else clauses.

❏ Assignment with modifiable display (=>)The modifiable assignment statement is identical to the assignment statement exceptthe result is displayed in the Experiment Tool and you can adjust the value. The userinput window takes on different forms depending on the type of parameter:

input box

constrained input



list box

select enumeration

❏ Assignment with display only (=?)The assignment with display statement is identical to the assignment statementexcept the value is only displayed and cannot be changed by the user. These itemsare shown as labels in the experiment tool.

label

Examples of assignments

Stringsfilename => “nmr_spectrum”;x_domain => 'Carbon13';

Numeric values (integer or real)scans => 8;define relaxation_delay => 3.0`[sec];

Expressionsdefine x_pulse => x90/2;

Enumerationsdefine evolution => “1/4J”, (“1/4J”,”2/4J”,”3/4J”);define multiplicity => “CH”, (“CH”, “CH2”, “CH3”);

Rangesdefine x_angle => 45`[deg], 1`[deg] -> 360`[deg] :1`[deg];define dept_pulse => 45`[deg],45`[deg]->135`[deg]:45`[deg];

Booleanauto_gain => false;



Current parameter value reference (#)

The # symbol is used to reference a current hardware parameter value. Forexample, if a sample in chloroform-d is locked and shimmed, the lock solvent wasalready input in the Sample Tool. When the Experiment Tool is initialized, thesolvent value in the experiment should be set to chloroform-d. This automaticsubstitution behavior is achieved using the syntax:

solvent => “#”;

The # symbol automatically references the hardware parameter of the same name.

Experiment Parameters

The experiments have several pre-defined parameters. These parameters areinitialized using assignment statements. Not all of these parameters are used in allexperiments. Each predefined experiment parameter -- i.e. every parameter that’s inthe header, acquisition or pulse section -- can optionally be given user-defineddefaults in the .delta_configure file.

These predefined experiment parameters cannot be changed with the PreferencesTool. Each parameter can be given its default value in the file by preceeding theparameter name with "experiment .". For example, to set a parameter for the scanparameter, you might write "experiment .scan = 16". The only exception to this ruleis the sample_id. If you write "experiment .sample_id = time", then the currentsystem time in tenths of seconds will be used as the sample_id time in theexperiment.

Table 10-2: Experiment Header Parameter Definitions

HeaderSection

Default Parameter Control Description

comment --Experiment comment, placed in the content field of thecollected file.

destination *

A string that lists the potential target nodes that willreceive the completed experiment. Only one system willactually get the experiment. An * in the list indicates thesubmitting workstation.

filename --The default filename is provided in the following format:YYYYMMDD_nD_sample_id_num.num.



filter_limit 0 Sets the oversampling factor for digital filtering.

filter_start 0 Sets the starting axial position for digital filtering.

filter_stop 0 Sets the ending axial position for digital filtering.

init_group 0Determines which init_group of pre and post instrumentconditions are used.

probe_attr --If omitted, then the experiment domains are appended. Itis used to help select the correct probe for theexperiment.

process --

The name of the Percival macro or program invokedafter collection. The resulting filename is appended tothe end of this line and it is spawned on the workstationthat received the completed experiment.

sample_id --Used for sample tracking and automation queuemanagement. If omitted, a unique number is generated.

slot 0 Changer slot on which to run the experiment.

sn_border 100

Number indicating the percentage of the max value usedas the highest point to be searched for a 'signal' peak.Omits the region around the center of the spectrum andthe region about the largest peak.

sn_noise_start 0Starting point of the region used to determine thespectral noise.

sn_noise_stop 0Ending point of the region used to determine the spectralnoise.

sn_ratio 0

Number indicating the desired signal/noise ratio of thedata. The experiment will terminate when this value isreached. A set value of 0 for the sn_ratio deactivatesthe calculation.

sn_signal_start 0Starting point of the region used to determine the signalintensity.

sn_signal_stop 0Ending point of the region used to determine the signalintensity.


HeaderSection




sn_skip 10Number of scans to skip before starting to check forsignal to noise.

start_time currentA string in the format DD-MTH-YYYY HH:MM:SSthat indicates at what time (instrument time) the jobshould be started.

Table 10-3: Experiment Acquisition Parameter Definitions

AcquisitionSection


mod_return 0Number of vectors skipped between vectors returned tothe workstation. Also determines how often signal-to-noise ratio should be sampled.

scans 1

Number of scans to collect. 0 results in 32K scans.Negative numbers result in outer scans on 2-dimensionalacquisitions. If the experiment is 1-dimensional, theouter scans are converted to normal scans and the

maximum value is 230

(1,073,741,824).

CHAN is an RF channel (IRR,TRI)

CHAN_domain

Sets a “non-observed” channel to a domain. Used whenan experiment requires a decoupling frequency, but thedecoupling frequency is not used as a multidimensionaldomain.

CHAN_freqSets a “non-observed” channel to a specified frequencyMHz.

CHAN_offsetAn offset from the base frequency of the CHAN_domainor CHAN_freq in Hz or ppm.

n is a domain (x,y,z,a,b,c,d,e)

n_points 1 Number of points to collect in each dimension.

n_prescans 0 Number of prescans before starting to collect.


HeaderSection




Define statement

The define statement is used to create new variable names for use inside the experiment. Avariable must be initialized with an assignment statement when it is defined.For example:

define relaxation_delay => 1`[sec];

StringsString values must be enclosed in matching quotes, either matching single quotes ` ` ormatching double quotes ““.

n_sweep 0Sweep width each dimension in Hz or ppm. This will becorrected (adjusted) at run-time for actual NMR ADCdwell period.

n_domain String indicating the desired nucleus for the domain.

n_freqOverrides the n_domain by forcing a specified MHzvalue.

n_offsetAn offset from the base frequency or domain in ppm orHz.

Table 10-4: Experiment Pulse Parameter Definitions

Pulse Section Default Parameter Control Description

module_config

A string that allows various special module features tobe controlled (see Pulse section description). themodule_config line in the experiment must specify the"lock_switch" option. This causes the pulse compilerto actually configure the head_amp to use the lockswitch device.

total_time

Indicates the total run time of the job. This is used forscheduling.

Note: a job of time 0 is assumed to takeinfinite time.

Table 10-3: Experiment Acquisition Parameter Definitions

AcquisitionSection




Units

The Delta software uses unit types throughout. The unit symbol is the single backquote `.The unit type is enclosed in brackets [ ]. Consult the Delta Programmer’s ReferenceManual for more information on units.

Align

The align statement takes all statements between the align and end align, and breaksthe total time into unique discrete times according to the modifier. The align statementtakes three modifiers - leading, center, and trailing. The order of the times is not important.The precision of the resulting pulses is limited by the pulser hardware. The align statementis most useful for centering pulses of different lengths from multiple channels, i.e.

simultaneous 180o pulses from observe and decoupler channels.

For example:

align centerx_pulse*2, (obs.gate, obs.phs.phase_1);y_pulse*2, (irr.gate, irr.phs.phase_2);

end align;

align trailingx_pulse, (obs.gate, obs.phs.phase_4);y_pulse, (irr.gate, irr.phs.phase_5);

end align;

Macro

Macro statements are similar to subroutines. Macros must be defined before they are usedand they may be loaded from include files. The syntax is

macro name (optional input variables) is....end name;



For example:

macro mlev (pulse_90, phase) is....end mlev;

Note that there is no “;” after the is statement. The input variable names in a macro areself-declaring and do not need to be defined separately. Variables are passed into a macroin the order listed when the macro is called. Take care to ensure that the variable ordermatches the macro declaration. To use a macro from inside a pulse sequence, the syntax is:

macro_name (optional variables);

For example:

mlev (x_pulse, phase_lock);

Loop

The pulse sequences have looping capability. The maximum value for a loop is 4095.Loops may be nested up to 7 levels.

loop value times....end loop;

Note that there is no “;” after the times statement.

For example:

define loop_number = 4;loop loop_number times....end loop;

Begin

The beginning of a pulse sequence is marked with a begin statement. All statementsfollowing the begin are interpreted as time states in the pulser. The pulse sequenceterminates with an end pulse; statement.

Conditional if-then-else statements

In the experiment file, if-then-else logic is supported. The if-statements can beused only in define statements and assignment expressions. The syntax is



define variable = if condition thenexpressions

elseother expressions;

If-then-else statements may be nested:if condition_1 then

expression_1if condition_2 then

expression_2else

other_action_2else

other_action_1

The Eclipse spectrometer does not support runtime conditional if statements in the pulsesequence.

INCLUDE FILES

The include statement, "include “filename,” lets an experiment loadadditional files into an experiment at compile time. Include files are incorporated andexpanded in the experiment just as if text were included in the original file. The bestcandidates for include files are commonly used sections of experiments or extensivemacro functions used in many different experiments.The syntax for an include file is:include “filename”;

User Include Files

Users may have their own private include files in their own experiments.

Standard Include Files

Standard Include Files

The standard global include files for experiments are listed in Appendix A.

std_headerstd_instrumentstd_dec_instrumentstd_solid_instrumentstd_acquisitionstd_2d_acquisitionstd_3d_acquisition

Header Section


All user written experiments should include these files for compatibility.

Include files are expanded in the experiment when it is read into the Experiment Tool.Include files are useful for standardizing the format of experiments and adding globalmodifications to the experiments. All of the JEOL-distributed experiments reference thestandard include files. User-written experiments should reference the standard includefiles for compatibility.

Set up properly, one could use include files to change an experiment parameter in all theexperiments on a spectrometer. For example, to add the slot parameter for an autosamplechanger, the System Manager would change the std_header file, which wouldimmediately add the header flag to all experiments.

HEADER SECTION

The Header section includes the basic attributes of the sample, data collection, and datastorage. A typical Header is shown in Figure 10-4. The Header is composed of list boxesfor string names and radio buttons for feature control.

Figure 10-4. Experiment Tool Header

filename

The filename is the string indicating the name of the file containing the data after



collection. In this field, enter a filename. If a file of the same name already exists, a newfile with a unique version number will be created, so the existing file will not beoverwritten. Do not use slashes, brackets, dashes or spaces in the filename.

Note: the filename does not include the version number. The Delta programappends the version number automatically based on how many other files ofthe same name exist. If a filename is left blank, the software will create aunique name composed from the data and time when the acquisition finishes.

sample_id

The sample_id is a unique string which identifies the particular sample. In this field,assign a sample name to differentiate among measurement samples. If the sample id is leftblank, the software will assign a unique number. Many features of the spectrometer queueuse the sample_id. The software depends on the sample_id in makingassumptions about queue control and automation. In the queue, if two experiments havethe same sample_id, the software assumes the correct sample is already in the magnetand will not load, lock, and shim for the second experiment. If multiple experiments arerun on the same sample, the sample id should be the same.

comment

The comment is a free format field in which you may enter information relative to thesample or experiment. No special syntactical rules apply to this field.

process

The process field is the name or command of the program or macro to be invokedwhen data collection is completed. The standard process lists are automatically set. If it isblank, the data is simply written to disk.

Table 10-5: Header Process Information Options

process_oned Invokes the process_oned program.

process_ndimensional Checks the data and invokes process_onedfor 1-D data and process_ndimensional forall other data.

process_global'process.list':

Invokes the 'process.list' name processinglist in the global process_list directory.

process_local'process.list':

Invokes the 'process.list' name processinglist in the user's local process_listdirectory.

Header Section


Autosample Changer slot

On systems with an automatic sample changer, the slot parameter determines thelocation of the sample for that particular experiment. On systems equipped with anautomatic sample changer, add the following line to the std_header file. This willadd slot control to all experiments.

slot => 0;

Header Flags

Header flags control (on/off) various features in the spectrometer and acquisitionconditions. Only some of the header flags are shown to the user; others are set in thestd_header include file. If the flag is not initialized, the default values apply.

Header flags demonstrate the use of the std_header include file to quickly customizeall the experiments for a site. To remove, add, or change the default value of a HeaderFlag, make the change in the std_header file and all of the global experiments willreflect the change.

Experiment Flags Legend

T = TrueF = FalseS = StringI = Integer

Table 10-6: Header Flags

Name Default Action when the Flag is set to TRUE

allow_copy T Enables copy of data during acquisition.

auto_dwell T When set to TRUE, the acquisition dead time and delaywill be automatically calculated; when FALSE, the usermust supply these values.

auto_filter F Causes the acquisition to digitally filter the dataautomatically within the maximum sampling rate.

auto_gain FCauses the recvr_gain to be automatically set beforethe data is collected.



automatic F

Runs these machine files that contain instrumentparameters and that are found in the /eclipse directory onthe acquisition computer:

machine.defaults for Experiment Initialization.machine.pre_exp for Data Collection, andmachine.post_exp

for Experiment Finalization.

create_file TCreates an output file for the collection. The vectorflag is respected.

destination SUploads data to a workstation defined in the string. Thisworkstation must have Delta installed on it, and youmust have an account on it.

eject FCauses the sample to be ejected upon completion of theexperiment.

filter_limit IDigital filter limit based on FILTER_LIMIT set inmachine.config.

filter_start S Start point in [ppm] or [Hz] for digital filtering.

filter_stop S Stop point in [ppm] or [Hz] for digital filtering.

filter_wide F Uses inverse Chebychev instead of elliptical Jacobiandigital filter.

force_tune F

Sets the autotune to be done regardless of previouslytuned domain. When FALSE, if the domains match, thenprobe is not retuned. In the case of a manually tunedprobe, the spectrometer is set to tune mode and the usermust tune the probe and acknowledge it on the screen.

force_vector F

Forces EVERY vector to be returned for the vector viewregardless of timing constraints. When FALSE, if the lastvector has not finished the process and display functionsbefore another acquisition begins, that vector is skipped.

hold F Causes the queue to be 'held for another job.



Header Section


init_group ICalls specific machine.defaultsx,machine.pre_expx machine.post_expx (x= 0 -> 9)

job_group FMakes this job part of a collection of jobs that will bescheduled together. The pre and post files will only berun before the first and after the last file in the group.

load_pulser TAcquires and downloads a pulse program. If FALSE,delay for total_time and then stop. Don't downloadthe pulse program.

load_shims F Causes the shims to be loaded for the experiment.

lock_check F Aborts the experiment if the lock is lost.

match T Waits for probe and/or sample checks.

multi_file FCauses the last arrayed dimension to be returned inseparate files instead of a virtual dimension nD file.

not_owned FWhen TRUE, the experiment will not run until theexperiment’s owner no longer owns the queue.

pre_post T Runs the pre and post instrument initialization files.

probe_attr SExecutes an experiment only if string matches any valuefrom the first line of the probe file.

quick_tune FOn autotune probes, use the quick tune feature instead offull tune.

repeat F Repeats the experiment until told to stop.

resubmit FResubmits the experiment when 'ok' is pressed untilaborted.

round_points TRounds the point values in dimensions greater than 1 tothe next greater or equal power of 2. The x_domain isalways rounded.

save_aborted FIf an experiment that collects a file is aborted, saves anduploads the file instead of deleting it.

sawtooth F Invokes the special sawtooth mode.





Header Parameters

In addition to the Header Flags, there are Header Parameters that also control variousfeatures and acquisition conditions. Only some of the Header Parameters are shown to theuser; others are set in the std_header include file. If the parameter is not initialized, thedefault values apply. (See Table 10-2 for a complete listing of these parameters.)

settle_vt

When set to TRUE in the experiment header, thetemperature control is turned ON, the instrument waitsfor the value of TEMP_SET (sample temperaturesetpoint) to be reached and settled before beginning theexperiment.If set to TRUE with the temperature control OFF, awarning message is given and the experiment proceeds.The temperature settling process may take up to 10minutes. A warning message is given and the experimentproceeds regardless of the outcome of that process.

slot I Sample changer position.

sn_border I Maximum s/n value for the data.

sn_noise_start I Start point for noise used in s/n calculations (ppm/Hz).

sn_noise_stop I Stop point for noise used in s/n calculations (ppm/Hz).

sn_ratio IValue of s/n ratio when achieved will terminate theexperiment. Set to zero to turn off s/n checking.

sn_signal_start I Start point for signal used in s/n calculations (ppm/Hz).

sn_signal_stop I Stop point for signal used in s/n calculations (ppm/Hz).

sn_skip I Don't stop experiment for s/n ratio below this value.

start_time SStarts experiment at a specified time. The time clock isthe acquisition system not the workstation. Syntax: dd-MMM-YYYY hh:mm:ss (13-FEB-1997 12:50:45)

vector FSends back real-time vectors for viewing (seeforce_vector).



Instrument Section


Adding Header Flags and Parameters Dynamically

❏ To add Header flags and parameters to the Experiment Tool:

1. Click on the name Header in the Experiment Tool window.2. A new window will appear on the screen (Figure 10-5).3. Select the header fields you want to include, clicking Add after each selection.4. When you are finished, click Done and the Experiment Tool will redraw to show the

new fields.5. For example, you may want to control the use of the Copy function, disallowing copy,

by default, for automation experiments. To do this, select the allow_copyexperiment header parameter on the header parameter list that pops up when youselect the Header title in the header window. Make sure the check box is uncheckedand press the Add button, then press the Done button.

Figure 10-5. Adding Header Fields

INSTRUMENT SECTION

The Instrument Section (Figure 10-6) contains all of the spectrometer hardwareparameters. Hardware parameters are those that have a direct correspondence to physicalhardware controls or attributes. The full list of parameters is in Appendix B: “InstrumentParameters”. All of the hardware parameters can be viewed and changed using the



Parameter Viewer on the Spectrometer Control Tool.

The hardware parameters are all pre-defined and may be used in assignments andexpressions. Only the most commonly used parameters will be discussed here.

Figure 10-6. Experiment Tool Instrument Section

Solvent

The solvent is the deuterated lock solvent, which you normally set in the Sample Tool.Otherwise, you may select one from this list. The solvent parameter is used for setting thelock offset frequency, lock power and lock gain. The default values for each solvent are inthe solvent.def file. If the solvent parameter is not set correctly, the auto-referencevalues may be incorrect.

Receiver gain (recvr_gain)

The receiver gain determines the amplifier gain on the receiver. It should be optimizedmanually or by using the auto_gain header flag. Normally the receiver gain isadjusted so one scan fills 50% to 80% of the ADC range. Running the ADC at a lowerreceiver gain will only slightly affect the dynamic range of the data. Over-running theADC by using too large a gain will cause the FID signal to be clipped. If the automaticgain setting is not used, set the receiver gain.

Instrument Section


Temperature control (temp_state and temp_set)

Temperature control may be performed either from the Sample Tool, or from individualexperiments.

If the temperature settings or modes from the Sample Tool and the ExperimentTool contradict, the Experiment Tool has priority. For example, if the NMRsample has stabilized at 50o C, then an experiment is submitted with the TEMPSTATE OFF, or, if TEMP_SET = 70oC, the spectrometer will adjust to the newconditions before running the experiment. If the experiment does not changethe temperature settings, i.e. neither the TEMP_STATE or TEMP_SET arespecified either visible or hidden, the experiment will continue with the currentsettings.

The order of the parameters in the Experiment file is important. The TEMP_SET valueshould precede the TEMP_STATE. Thus the value in the set temperature register shouldbe initialized before the temperature control command is issued.

Audio filter type (filter_mode)

The Eclipse spectrometer supports two type of analog audio filters, Butterworth andBessel. For most spectroscopy they can be used interchangeably. Butterworth filters willproduce a slightly larger first-order phase error near the spectral edge. Bessel filters moreeasily adjust a “dish” effect or DC offset in the baseline.

Table 10-7: Temperature Parameter List

Parameter Function of the Temperature Parameter

TEMP_STATE Variable temperature state ON or OFF

TEMP_GET Current temperature

TEMP_SET Desired final temperature

TEMP_COMP Compensation value - usually 0

TEMP_DELAY Time delay to wait for sample equilibration after the variabletemperature unit has reached the target temperature

TEMP_LIMIT_HI High temperature limit for the probe in the *.probe file

TEMP_LIMIT_LO Low temperature limit for the probe in the *.probe file



Adding Instrument Parameters Dynamically

❏ To add an instrument parameter to the Experiment Tool:

1. Click on the Instrument title in the Experiment Tool window.2. A new window will appear on the screen (Figure 10-7).3. Select the instrument fields you want to include, and click Add.4. When you are finished, click Done and the Experiment Tool will redraw to show the

new parameters.

Figure 10-7. Adding Instrument Parameters

ACQUISITION SECTION

The Acquisition section of an experiment (Figure 10-8) most closely resembles atraditional parameter file. The acquisition section contains information about the NMRfrequencies, sweep widths, data points, etc.

Acquisition Section


Figure 10-8. Experiment Tool Acquisition Section

DomainsEclipse experiments use the concept of a domain. A domain is the NMR nucleus orfrequency associated with the data sampling in a particular dimension. Usually the nameof the nuclear species is used instead of the frequency, thus removing the instrument/magnetic field dependence from the experiment. The instrument frequency (MHz) for adomain is calculated from the field strength in Tesla (in the machine.config file) andthe gyromagnetic ratio (in the gamma.def file). Domain order progresses from x to e inthe order (x,y,z,a,b,c,d,e).

x DomainThe x_domain is the observed NMR signal which is digitized in the A/D converter.You may select the nucleus to be observed.

y and Higher DomainsDomains labeled y or higher (y,z,a,b,c,d,e) are higher dimensionality nuclei,indirectly observed by the experiment. They can be the same as the x_domain as in aCOSY or different as in a CH correlation.

Spectral OffsetThe domain specifies the particular nuclear base frequency. In this field, you may set theobservation center frequency (ppm). Often it is necessary to shift the spectral center to



observe another part of the spectrum or to optimize the spectral width for a multi-dimensional experiment. The spectral center is determined by domain offset parameters.Each domain in an experiment may have an offset. The gamma value in the gamma.deffile is adjusted to set the center of the spectrum to the 0 ppm chemical shift reference valuewith 0 ppm x_offset. To shift the spectral center to 5 ppm, the x_offset is enteredas 5 [ppm]. Offsets may be entered in Hz or ppm units. The actual calculation andconversion of the domain and offset parameters is done at run-time in the acquisitionsystem.

Spectral (Sweep) WidthsThe spectral width in a particular domain is determined by domain sweep parameters. Inthis field, you may set the observation range (ppm). Each domain in an experiment musthave a value. The Eclipse NMR has a dual channel, simultaneous sampling acquisitionsystem. Therefore the x_sweep is given as the total observed spectral width instead ofthe plus/minus sampling frequency (i.e., 2000 Hz is really +1000Hz). This value can beentered in ppm or Hz. If the value is entered in ppm, it is internally converted into Hzimmediately prior to acquisition.

Data PointsEach domain must also have the number of data points to collect. This is done with thedomain points statement. In this field, you may set the number of data points of the f2axis. The x_points value must be a power of 2 (for the FFT algorithm). A non-powerof two value will automatically be increased to the next higher power of two duringcollection. The behavior for higher dimensions (y_points, etc.) is determined by theround_points header flag.

On the Eclipse, x_points always represents the number of complex pairs, i.e.x_points = 16384 is 16384 complex numbers, each with a real and imaginary part,for a total of 32768 values.

For higher dimensions, this value is the number of slices or planes. The collection mode,real or complex, specifies how the data is collected and may impact the experiment time.

ScansThe scans parameter determines how many times through the pulse sequence theacquisition will repeat. In the field, you may set the number of accumulations. Forexperiments, scans are per slice and not affected by y_points. The maximum numberof scans depends on the usage and experiment. Scans may be either positive (inner scans)or negative (outer scans). For one-dimensional experiments there is no difference, exceptthat the maximum limit is different.

For multi-dimensional experiments positive (inner) scans means each slice (timeincrement) is time-averaged for scans times before incrementing to the next slice(conventional 2D acquisition). Negative (outer) scans means after each single acquisition,the counter is incremented to the next slice, and then scans number of passes is madethrough the entire data set.

Pulse Section


PrescansPrescans are the number of times through the pulse sequence before the data collectionbegins. With this field, you set the number of prescans (dummy scans). The data isdiscarded after prescans. For one-dimensional data, x_prescans is used. For two-dimensional data, both suppressions and y_prescans may be used.x_prescans is executed only on the first slice and y_prescans is used for theremaining y_points. Normally, y_prescans is not required because there is nodelay going from slice to slice in a 2-D experiment, and therefore the equilibriummagnetization does not change.

mod_return is a number specifying how often the acquisition data is returned to theworkstation and the View tool. If it is 0, then the View Tool never updates.

y_points specifies the number of points in the y dimension of a 2D or 3D experiment.This is often referred to as the number of “slices”, or “t1 increments”. No compensation isnecessary for hypercomplex (Phase sensitive) 2D experiments. The value of y_pointscan be altered by the round_points header flag. If round_points = TRUE, theny_points will be rounded to the next higher power of 2 when the experiment is run.

x_acq_timey_acq_timex_resolutiony_resolution

These values are calculated by the std_acquisition include file.The formulae are:x_acq_time = x_points/x_sweepx_resolution = x_sweep/x_pointsy_acq_time = y_points/y_sweepy_resolution = y_sweep/y_points

PULSE SECTION

The Pulse section of the experiment (Figure 10-9) contains the pulse sequence and virtual

Table 10-8: Scans Parameter Limits

scans maximumone-

dimensionaltwo-dimensional

positive 1073, 791, 824 1073, 791, 824 inner scans 32768 max

0 ... forever 32768

negative -1,073,741,824 1,073,741,824 outer scans 32768 max



parameters for the timing of the pulse sequence. Experiments use the concept of virtualparameters. A virtual parameter is usually a time and does not correspond to a hardwareparameter, such as a gain or frequency. Virtual parameters exist only within an experimentand are for the convenience of the operator. Virtual parameters may be defined, used, andreferenced within an experiment.

Figure 10-9. Experiment Tool Pulse Section

total_timeThe approximate time necessary for measurement is displayed.

x_pulseThe pulse width actually used for the measurement is displayed.

relaxation_delaySet the delay time.

j_constantSet the J value.

❏ To view the graphical representation of the Pulse sequence:Click on the Pulse button within the pulse section in the experiment tool.This brings up the pulse display widget (Figure 10-10). This widget graphically displays

Pulse Section


information about the experiment currently loaded into the Experiment Tool. The pulsewidget is for display only; it can not be used for entering experiment information, or formaking modifications to the pulse sequence.

Figure 10-10. Pulse Display WidgetThe pulse display widget consists of three sections: loop, header, and chart. Solid linesare used to resize individual areas of the chart widget, so that greater or lesser portions ofit may be used to display the chart, loop, or header section. Drag the square on the rightedge of these bars up or down to change the size of a portion of the widget.

In the bottom section, the opening and closing of individual gates within an experimentare displayed. The label to the left of each row of the chart indicates the gate. The labelsplaced horizontally above the chart show which instruction is being acted on, and howmuch time this instruction should take. The numbers below these horizontal labels simplyindicate the chronological order in which they are carried out. The letter ‘m’ appearsbefore the number on those instructions which are macros. Instructions containing arrayedvalues appear with the letter ‘a’ displayed next to their number. The buttons to the left ofthe horizontal labels are for acting on the macros, which may be expanded or shrunkindividually, or all at once.

At the top of the widget are two empty boxes. Clicking on an individual pulse value will



cause its instruction, any arrayed values, and the time that it will take to appear in thetopmost box. Some of the pulses are given multiple angle values; these are outlined.Clicking on an outlined pulse will cause the values of these angles to be displayed in thelower box.

Finally, there is a section for displaying the presence of loops within the experiment. Ifloops are present, they will appear beneath the boxes at the top of the widget. Loops aredisplayed as solid lines above whichever instructions (including other loops) they enclose.These lines are labelled with as much of the name they were given in the experiment file aswill fit beneath the line representing them.

SUBMITTING EXPERIMENTS

Verify the settings of the Header, Instrument, Acquisition, and Pulse section fieldsagain. If they are correct, click on the Submit button in the Experiment Tool window toenter the experiment into the Spectrometer Control computer’s queue. By this operation,measurement starts.

Note: The command for starting an experiment can be issued repeatedly, evenif another experiment is currently being collected. After one experimentfinishes, the next experiment will be started under the stored experimentconditions. In other words, the spectrometer executes experiments on a first-in,first-out basis.

Probe Codes and Probe Files

Each type of probe has a unique identification code that the spectrometer senses throughthe Probe Status connector displayed in the Sample tool. This code number is used to lookup a probe file specific to a given probe. Each probe file contains unique information aboutthe probe. This information may be accessed and used inside an experiment.

The spectrometer probe files are normally found in the /eclipse/probes/ directoryon the acquisition system. You must have root privilege on the acquisition computer to editthe probe files. The codes for common probes are listed in Table 10-9.

Submitting Experiments


For GX, GSX, and CPF spectrometers retrofitted with a Delta Upgrade, theprobe codes will be different because only the 8 lower bits are read.

The standard GX, GSX and CPF assignments are given below.

Note: these are standard CPF values, but they may vary on differentspectrometers.

Probe AttributesThe first line in any probe file lists the probe attributes. These attributes are used with theoptional probe_attr field in the Header section. The software also uses this string tocheck for compatibility between the domains (frequencies) requested and the allowablefrequencies on a probe. If the software detects an obvious conflict, such as a 13Cx_domain on a 1H only probe, the experiment will abort.

90 Degree Pulses

The default 90o pulses are accessed for viewing only in the Spectrometer Control Toolunder Tool-90s:

Table 10-9: Eclipse Probe Code List

Probe Code Probe Description

1412 Standard 5mm TH5 Broadband probe 31P-15N

1288 10mm T10 Broadband 31P-15N

1320 10mm T10L Low frequency 15N-103Rh

1556 5mm 1H

1796 5mm HX5 Inverse 31P-15N

2564 Autotune 5mm TH5 Broadband probe 31P-15N

Table 10-10: GX, GSX and CPF Assignments

Probe Code Probe description

53 Standard 5mm TH5 Broadband probe 31P-15N

34 10mm T10 Broadband 31P-15N

5 5mm CH Dual probe

69 5mm 1H

93 5mm HX5 Inverse 31P-15N



90 = 10.0 10.0 50.0

The order of the values is -> observe, high power decoupling (HI), and low power

decoupling (LO). These are the default 90o pulse widths and are used when no matching

domain (nucleus) is found in the probe file. If a matching domain is found, then the 90o

values inside the domain are used.

Spin Lock PulsesThe spin_lock_90 and spin_lock_attn parameters are used for setting theparameters for spin lock experiments such as HOHAHA or TOCSY. These spin lockvalues are always calibrated pairwise, that is for a spin_lock_90 pulse, there is onlyone spin_lock_attn value.

Temperature LimitsEach probe may have a different approved variable temperature range. The variabletemperature controller may operate over a range larger than that approved for a particularprobe. The maximum range of the spectrometer is specified in the machine.configfile. The TEMP_LIMIT_HI and TEMP_LIMIT_LO determines the legal range for eachprobe.

The solvent.def file contains the boiling and freezing points for all of thestandard deuterated solvents. If the requested temperature exceeds either ofthese values, a warning message is displayed in the Delta Console and anacknowledge box is displayed.

Irr_codeThe irr_code value determines the maximum decoupler power during three different pulseconditions. The irr_code is a base 10 number derived from the octal (base 8). SeeAppendix C for details on how to calculate the values.The irr_codes for common probes are:

For GX, GSX, and CPF spectrometers retrofitted with a Delta Upgrade, onlytwo irr_codes are valid (only the lowest 3 bits are read). Therefore an irr_code

Table 10-11: IRR Codes for Probes

Probe Type irr_code

TH5 146

T10 212

T10L 212

H5 128

HX5 128

Submitting Experiments


<= 4 will deliver the “4 watt” level, an irr_code >= 5 will deliver the “9 watt”level.

DomainsThe domain sections of the probe files are used to store hardware parameters that arespecific to the particular nucleus. Any hardware parameters may be entered in the domainsections. The domain sections are denoted by the syntax:

domain nucleus....end domain

The most common values in the domain section are the 90o pulses. The order is the same

as the default 90o pulses - observe, high power decoupling, low power decoupling.

Probe Tuning ValuesThe domain section can also contain the probe tuning values for each nucleus. The tuningvalues are displayed when the force_tune header flag is true. The values are also used bythe autotune probes.



CALCULATIONS

Calculation of Pulse Widths and Angles

Referencing Probe VariablesThe pulse widths stored in the probe file are referenced in the following way:

“domain90_modifier”

where “domain” corresponds to the x,y,z,a,b,c,d,eand

“_modifier” corresponds to the HI, LO, or no decoupler power.Pulse widths for different nuclei are separated by the domain sections.

For example, consider the following statement:x_pulse => x90;

This statement means the following:• define a variable x_pulse (normally in keeping with good programming practice,

x_pulse would be related to the x_domain, but it could be called something else).• assign the value of x90 to x_pulse

x90 is a special hardware parameter. It refers to the first value in the set of threenumbers after the "90 =" in the probe file in whatever domain section matches the

current x_domain. Each time the domain changes, the new 90o values for that domainare read from the probe file.

A second example:x_pulse => x90/2;

This is similar to the first, but the x90 value is part of an expression (divide by 2).

A third example:y_pulse => y90_hi;

In this case the variable y_pulse (which would normally have something to do with the

y dimension of a 2D spectrum) is set to the second value in the set of three 90o pulses forthe nucleus specified by the y_domain.

A final example is:irr_pwidth = irr90_lo;

In this case, a hardware parameter irr_pwidth is set to the third value in the set of three 90o

pulses. In this case the nucleus domain is specified by the irr_domain.

Calculations


Using Expressions to Calculate Pulse Angles

The x90 values may be used as part of other expressions to convert pulse widths intopulse angles.

For example:define x_angle => 90`[deg], 1`[deg] -> 720`[deg] :1`[deg]define x_90_width => x90define x_pulse =? x_90_width * (x_angle / 90`[deg]);

In this example, x_angle is assigned to 90° and the legal range is from 1° to 720° in

steps of 1°. The displayed value is changeable by the user (=> symbol) in the ExperimentTool. The x_90_width is assigned to the x90 parameter from the probe file and is alsochangeable by the user. The x_pulse (the actual time duration of the pulse) is calculatedfrom the expression and only displayed (=? symbol) in the Experiment Tool.

Calculation of Audio Filter Delays

The Eclipse supports two types of hardware audio filters, Butterworth and Bessel. Someof the features of each have been mentioned previously. Following the final RF pulse butbefore the first data point is sampled, several things occur in the spectrometer. First, a timeis reserved to let the probe recover from the effect of the RF pulse and to compensate forany pulse breakthrough. This time is called the dead_time and all spectrometer gatesare closed.

Following the dead_time, a second time period is reserved to open the receiver andstabilize the electronics (i.e. audio filters) before sampling the first data point. This time iscalled the delay. Because the spins have begun to precess and evolve starting from theend of the pulse, the values of dead_time and delay can have great impact on the data.Normally, effects are seen in the spectral phasing and in baseline roll.



The Eclipse uses different formulas for calculating the dead_time and delaydepending on the audio filter type. These expressions are in the std_pulse include file.

define dead_time =if filter_mode = "BUTTERWORTH" then

if 0.6/x_sweep - x_pulse/2 < 15[us] then15`[us]

else0.6/x_sweep - x_pulse/2

else --BESSEL case20`[us];

define delay =if filter_mode = “BUTTERWORTH” then

if 0.4/x_sweep < 0.5[us] then0.5`[us]

else0.4/x_sweep

else --BESSEL case0.6/x_sweep;

Total Time

Every experiment includes a Total Time calculation. This calculation is performedautomatically by the Experiment Tool. The total time is used by the Experiment queuemanager for scheduling of the experiment using the rules assigned in the queue.hoursfile.

If the time calculation seems in error, check the collect statement and the number ofbuffers for the experiment.

PHASE TABLES

The RF signals from an NMR spectrometer may have frequency, phase, and amplitudecharacteristics. The frequency is controlled by the domain and offset. The phases arecontrolled by variables in the experiment. Once a phase variable is defined it may be usedmultiple times in a single experiment. Phases are defined as sets using the brace “{}”syntax. Refer to the section on multiple buffers for information on nested braces.

For example:define phase_1 = {0, 90, 180, 270};

Parentheses provide a shorthand notation for repeated phases:define phase_2 = {4(0),4(180)};

Phase Tables


This expands to:define phase_2 = {0,0,0,0,180,180,180,180};

Parentheses may also be nested:define phase_3 = {2(2(0), 4(180), 2(0)),

2(2(90),4(270),2(90))};

This expands to:define phase_3 = {2(0,0,180,180,180,180,0,0),

2(90,90,270,270,270,270,90,90)};

Which, upon further expansion, becomes:define phase_3 = {0,0,180,180,180,180,0,0,

0,0,180,180,180,180,0,0, 90,90,270,270,270,270,90,90, 90,90,270,270,270,270,90,90};

The maximum phase table length is 255 steps.

Concatenation of Phase Sets

Using the concatenation operator “||”, multiple sets of phases may be concatenatedtogether.

For example:define a = {0, 90, 180, 270};define b = {270, 180, 90, 0};define phase_1 = a||b;--The result of the define phase_1 is:--phase_1 = {0,90, 180, 270, 270, 180, 90,0}

Addition of Phase Sets

A constant value may be added to any phase. The addition is distributed across the entireset of phases.

For example:define a = {0, 90, 180, 270};define phase_1 = a+90;--The result of the define phase_1 is:--phase_1 = {90, 180, 270, 0}



90 Degree Phases

Most phase tables are constructed with quadrature (90o) steps.

For example:define phase_1 = {0,90,180,270};

Sub-90 Degree Phases

The Eclipse spectrometer can be equipped with sub-90o phase shifters. These are normally

30o, 45o, 60o within each quadrant. Therefore, phases of 0, 30, 45, 60, 90, 120,135, 150,

180, 210, 225, 240, 270, 300, 315, and 330o can be generated.

The phase sets are created in the normal way:define phase_4 = {0,45,90, 135, 180, 225, 270, 315};

Note: The sub-90o phases use additional hardware lines in the pulser. Thisassignment is done automatically by the experiment compiler. When sub-90o

phases are used it is possible to exhaust assignable pulser lines such that theexperiment will not execute.

MULTIPLE BUFFER ACQUISITION

In many experiments, multiple data collections are required while changing a singlevariable such as a phase and keeping the data in separate locations. Data collected in thisway are said to be “multiple buffer acquisitions”. The number of buffers is determined bythe nested braces around a variable. For example, a two-buffer phase experiment could bewritten as follows:

define phase_6 = {{0, 180}, {90, 270}};

The pulse sequence will cycle through all buffers on each scan, then increment the scancounter. Thus the total number of acquisitions is equal to scans * buffers. Incrementationof phases is done on scans, not buffers.

Multiple buffer acquisitions also use the collection mode for data routing inmultidimensional experiments.

For example:

define phase_1 = {{ 0, 180, 180, 0},{90, 270, 270, 90}};define phase_2 = {2(0), 2(180)};define phase_acq ={0, 180, 180, 0};

module_config Options


MODULE_CONFIG OPTIONS

Each module in the Eclipse spectrometer has options that can be set to achieve differentfeatures. These options are controlled by the module_config parameter. Because theoptions are often channel specific, they are labeled with the output channel.

Hardware Options

The module_config options are composed of a prefix.feature. The prefix isthe RF channel (OBS, IRR, TRI) for the particular feature. Multiple features may beapplied by adding additional strings. The order is not important. However, if any feature isset, all desired features, including .normal, must be set.

Table 10-12: Multiple Buffer Phase Cycles

buffer 1 buffer 2

scan phase_1 phase_2 phase_acq phase_1 phase_2 phase_acq

1 0 0 0 90 0 0

2 180 0 180 270 0 180

3 180 180 180 270 180 180

4 0 180 0 90 180 0

Table 10-13: RF Channel settings

Mode Function

CHECK Check mode, normally not used.

NORMAL Must be set if any non-check feature is set.

CW CW mode - RF on continuously.

ATN Attenuator on.

FINE_PHASE1 RF fine phase shift offset 1.

FINE_PHASE2 RF fine phase shift offset 2.

SPIN_ECHO Used in solids experiments.

SOLID_SHAPER Used in solids experiment, OBS only.

SOLID_SAMPLE Specifies there is a solids probe connected.The machine will enforce a match probe type (solids/liquids) and an export type (solids/liquids).



Table 10-14: Time-shared Homonuclear Decoupling

Mode Function

TIME_SHARE Activates RF time sharing.

CYCLE_10KHZ Cycles between the offset frequencies at 10kHz digital.

CYCLE_TIME_SYNCCycle between the offset frequencies synchronized withthe time-share pulse digital offset unit only.

Table 10-15: Noise Modulation Gating

Mode Function

IRR and TRI channels only

NOISE1 RF noise source offset 1 - noise modulation only.

NOISE2 RF noise source offset 2 - mod controlled by rf_mod.

Table 10-16: Amplifier Power Settings

Mode Function

AMP_NORMAL AMP normal power mode.

AMP_LOW_PWR Low power mode for amps.

OBS amp Only

ROUTE_IRR Route check mode from IRR through OBS.

ROUTE_TRI Route check mode from TRI through OBS.

IRR & TRI amp only

AMP_9W Enables 9watt mode (vs. 4watt default).

AMP_HOMO Enables homonuclear decoupler power mode.

AMP_BILEVEL Turns on bi-level power switching mode.

AMP_FULL_PWR Enables full power mode.

AMP_INEPTCHK Enables inept check mode.

Table 10-17: Combination Features

Mode Function Combinations

CW_NOISE NORMAL, CW, and NOISE1

Collection Mode


COLLECTION MODE

The COLLECT statement is used to ensure that the data is collected properly in eachdimension and referenced properly to the RF channel for the dimension. The order isimplied to be (x y z a b c d e). Each dimension is separated by a space, and the valueswithin each domain are separated by commas.

For example, a typical one-dimensional experiment can be written as: collect complex, obs;

The Eclipse always collects the x domain as complex vectors and normally the observechannel OBS generates the x_domain RF.

For a typical two-dimensional absolute value experiment:collect complex, obs real, obs; -- cosy

orcollect complex, obs real, irr; -- ch-correlation

For a phase sensitive two-dimensional experiment:collect complex, obs complex, obs;

By default the Eclipse presents all multidimensional data in a “p-type” format; i.e., the 0ppm (high field) coordinate in the upper right corner and the axis units increasing to thelower left corner as the operator views the data. If a phase cycle results in a reversedpresentation, use the NTYPE collection mode to reverse the sense of the axis.

collect complex, obs real, irr, ntype;

One could alternatively use the REVERSE Percival command during dataprocessing to correct the presentation.

MACROS

As discussed in an earlier section, the pulse sequences may reference macro programs,either from inside the experiment or via include files.A macro used in almost all experiments is the acq macro:

macro acq ( dead_time, delay, phase ) isdead_time, (reset);delay, (reset,rcv.gate);acquire (reset,rcv.phs.phase);

end acq;

HIGH_PWR NORMAL, NOISE2, and AMP_FULL_PWR

Table 10-17: Combination Features

Mode Function Combinations



PULSE PROGRAMS

Specifications

The Eclipse with the PGX-300 pulser has the following specifications:

Begin/end StatementThe pulse sequence is marked with a begin statement. The pulse sequence terminateswith an end pulse; statement.

Time StatesThe Eclipse pulse sequences are series of variables representing time delays followed by alist of gate assignments which describe the desired RF behavior during the particular timedelay. The delays are called time states. Each line after the begin statement representseither a time state, output gates, or both.

Referencing Time VariablesA variable is assigned to a time state by simply using the name:

begininitial_wait;

...end pulse

In this example, the time value previously assigned to initial_wait is executed.

Referencing Spectrometer ParametersA hardware time parameter, such as x90, may be used directly:

beginx90;

...end pulse

Table 10-18: PGX-300 Pulser Specifications

Pulse Control Specification

time state range 0.3 us to 429 sec

time state setability 0.1 us

time state precision 0.2 us

loop precision 0.3 us

jump precision 0.2 us

output gates 20

loop range 0 to 4095

Gate Assignments and Options


In-line CalculationsCalculations may be performed in the pulse sequence. The calculations are evaluatedwhen the experiment is compiled just prior to execution.

begin...

1/(2*j_constant);...end pulse

In this example, the time delay will be the reciprocal of twice the j_constant variable (Hz).Note that the parentheses are required to order the mathematical operations properly.

End of SequenceAt the end of the pulse sequence, all gate lines are closed before the jump back to thebeginning of the sequence.

GATE ASSIGNMENTS AND OPTIONS

The gate assignments controlled by the pulser are directly wired to various hardwarefeatures. Each time state may be followed with the gate conditions during that time state.The gates remain open only for the duration of the time state. To set a gate on or off formultiple time states, use the ON or OFF statement. The ON or OFF statement can be usedto set conditions without a time state.

The Eclipse has a total of 20 output gates. Many of the output lines have fixedassignments; others are automatically assigned by the Experiment compiler.The general syntax for gate conditions is:

time_state, (channel.feature.variable);

Note: the comma after the time state is required. If the comma is missing, asyntax error will occur and experiments will not compile.

Multiple gates on a single time state are specified by listing them inside the parentheses:time_state, (channel.feature.variable,

channel.feature.variable,...);

The on and off statement syntax is:on (channel.feature.variable);off (channel.feature.variable);

Multiple gates may be listed inside the on and off statements.

Note: There is no comma after the ON or OFF.



RF GatesThe RF gates are called by using channel.gate.

For example:obs.gateirr.gatetri.gate

RF PhaseThe RF phases are called by the channel.phs.variable, where channel is one ofthe RF channels and variable is the name of a phase list.

For example:obs.phs.variableirr.phs.variabletri.phs.variable

AttenuatorsEach of the RF channels has a variable attenuator. The attenuator values range from0[dB] (no attenuation) to 64[dB] (maximum attenuation, minimum power) in 0.125 dBsteps. The attenuator value must be defined as a virtual parameter.

For example:obs.atn.variableirr.atn.variabletri.atn variable

Note: The Experiment compiler automatically detects the use of an attenuatorand sets the module_config parameters accordingly.

Frequency OffsetThe RF may be switched between two frequency locations using thechan.offset.variable. The channels are limited to the decoupler channels.For example:

irr.offset.variabletri.offset.variable

Noise ModulationEach of the decoupling channels can be modulated to provide broadband decoupling. Themodulation parameters are listed as hardware parameters and the modulation sequence areprogrammed in ROM.

Gate Assignments and Options


The noise modulation is controlled separately from the RF gate. The default condition ofall experiments is noise modulation off. To activate continuous noise modulation use themodule_config variable chan.noise1.

For example:module_config = “irr.normal, irr.noise1”;

This method sets the modulation on continuously, but the RF gate is controlledindependently.

Other experiments require the pulse sequence to switch from CW to noise modulationduring the sequence. This is done using a combination of the module_config andrf_mod gate line:

module_config = “irr.normal, irr.noise2”;...on (irr.rf_mod); -- activate noise

off (irr.rf_mod); -- deactivate noise

Acquisition MacroThe acquisition macro controls specific gate lines - reset, rcv.gate, rcv.phs.The reset line initializes the counters and phase tables for acquisition, the rcv.gate lineopens the receiver, and the rcv.phs.variable controls the receiver phase.

macro acq ( dead_time, delay, phase ) isdead_time, (reset);delay, (reset,rcv.gate);acquire (reset,rcv.phs.phase);

end acq;

Interactions with irr_code and module_configIf the AMP_FULL_PWR mode is invoked in any of the module_config options, thepulse power level is determined by the first value of the irr_code parameter. In order to

Table 10-19: Irradiation Modulation Modes

Mode Description

IRR_PWIDTH 90o pulse width at the IRR decoupler power level

IRR_NOISE IRR noise modulation - Waugh, Waltz, Square wave

TRI_PWIDTH 90o pulse width at the TRI decoupler power level

TRI_NOISE TRI noise modulation - Waugh, Waltz, Square wave



protect the probe from excessive power (damage from arcing), a special hardware gate isused in high power sequences during the Decapolis period. The rf_limit gate is used todrop the decoupler power from the high power level to the acquisition level for decoupling(third value in irr_code).

For example:on (irr.rf_limit);...off (irr.rf.limit);

On GX, GSX, and CPF spectrometers (Delta Upgrade) the rf.limit bitdoes not work the same way on the irr channel. Therefore, ifamp_full_pwr is used in any way, an attenuator must also be used toreduce the decoupling power. On any Delta Upgrade spectrometer (GX, GSX,CPF) exercise extreme caution until the decoupler power levels areindependently measured with a power meter or an oscilloscope. Refer toAppendix D for more information.

COMPILING AND ERROR MESSAGES

When the experiment is loaded into the Experiment tool, the text is interpreted and theuser-changeable variables are displayed. If the Experiment detects an error in the file, anerror message will be placed in the screen and information about the error will bedisplayed in the Delta console window.

When the experiment is submitted to the spectrometer, it is held in the experiment queue.When the experiment comes to the top of the queue for execution, it is compiled into aform the pulser understands and then executes.

ARRAYED PARAMETERS

Often an operator wants to vary one or more parameters while repeating the sameexperiment. The Eclipse allows the operator to input an array of values into a singleparameter in the Experiment Tool.

An arrayed parameter allows you to collect multiple data sets while systematically varyingone or more experiment parameters. The data from an arrayed parameter experiment maybe stored as multiple files or as a single multi-dimensional file. The entire experiment isrepeated for each value in the array.

When the experiment is run, the acquisition system will detect the arrayed parameter as avirtual dimension.

Interaction with multi_file OptionIf the multi_file option in the header is true in an experiment, each separate datasetfrom an arrayed parameter experiment is returned as a separate file. If the multi_file

Arrayed Parameters


option is false, the arrayed parameter data set is returned as a single multi-dimensional filewith virtual dimensions.

The normal Delta processing tools may be used with the virtual dimension data sets,except for processing in a non-linear dimension.

SyntaxAn arrayed parameter may be created with most experiment variables by the arraycommand. The command is of the form y_acq, where y denotes that the array willbecome the y_domain of a pseudo-2D data set. Likewise an arrayed parameter for atwo-dimensional experiment is denoted by z_acq, thus creating the z_domain of apseudo-3D data set. Likewise, there are a_acq, b_acq c_acq, d_acq, ande_acq.

The array statements can be nested, the outermost array is performed before eachincrement of the inner arrays.

Following the array statement is the set of the arrayed values in brackets. The list can beeither discrete values, or a range with a step size, for example:

y_acq {5, 10, 15, 20}.

The Experiment Tool will check to see if an arrayed list can be expressed as a range. If itcan, then a range is displayed:

y_acq {5 -> 20 : 5}

Arrayed parameters are entered either directly in the Experiment Tool field, or in a pop-up window obtained by clicking on the parameter name.

For example:

Clicking on the “scans” parameter produces a window like the one on page 10-51, fromwhich the user may enter the array either as a set:

{value1, value2, value3,...}

or as a range with a

{start value -> stop value: step size}

When using parameters with units, at least one of the values must have a unit. If only oneunit is specified, the Experiment Tool applies that unit to all values. If different units aredesired, all values must have units specified.



After the array is entered, the parameter entry in the Experiment Tool will change to:

if the entered data can be ranged, or

if the entered data cannot be ranged. To modify an existing array, place the cursor in thewindow, or click on the parameter name.

If the array is too long to fit in the window, it scrolls off the edge. Use the Home and Endkeys to move from one end to the other.

EXCEPTIONS TO ARRAYED PARAMETERS

The only values that cannot be arrayed are parameters that affect the size ordata point sampling of the file. This includes domains, sweep widths,and points.

SETTING ARRAY PARAMETERS

The Set Array Parameters Window (Figure 10-11) comes up when you select aparameter that can be arrayed (otherwise, a simple box with the value which cannot bearrayed will come up). Parameters can be arrayed for an experiment of up to eightdimensions.

Use the Pick cursor mode to cut and paste values into the Set Array ParametersWindow from an open geometry with data. To remove a value from the value list, selectthe value and press the Remove button. Selecting Clear will remove all values from the

Collecting T1 Data


list. Use the Set Value button to update the arrayed parameters in the experiment. Cancelto cancel this setting. All available dimensions are displayed in the dimension box to theleft of the window; the top dimension is the default setting.

Array Types can be represented in Linear, Exponential or Logarithmic form, with Startand Stop values, and a Step increment. To bring up this screen, toggle off the Listed Box.

Figure 10-11. Set Array Parameters Windows

COLLECTING T1 DATA

Because the data set can only be collected in the x-y plane, we have to set up an array oftau values for the experiment to collect T1 data.

❏ To collect data for T1_analyze:Use either/usr/people/jeol/nm8901/global/experiments/1d_more_exp/double_pulse.exp

or/usr/people/jeol/nm8901/global/experiments/1d_more_exp/double_pulse_dec.exp

Note: double_pulse_dec.exp is used for carbon atoms.

1. First, try using the arrayed parameter pop-up box (click on the tau_interval button tobring up the pop up box.)

2. Or, enter the arrayed tau_interval parameter manually. The parameter is arrayed in thefollowing fashions: y_acq{0.1->20:0.5[s]}, i.e., 01[s] -> 20[s] in 0.5[s] steps. ory_acq{0.1[s], 0.2[s], 0.3[s]....} which sets the tau value explicitly. This arrayedparameter can be entered using the arrayed parameter pop up box (click on thetau_interval button to bring up the pop up box.)



3. Last, set up the rest of the parameters of the experiment as usual.

After the pseudo 2D data set is uploaded, use 1D slice to process the first slice and phasein the x_domain. Subsequently, the processing list along with the phase information isapplied to the remaining slices by sending the processed data to the data slate. Then thedata can be ported into T1 Analyzer for relaxation analysis.

DELTA User’s Guide, v 3.2 A-1

APPENDIX A: STANDARD INCLUDE FILES

The following files can be found in the /usr/delta/global/experiments/directory.

STD_ACQUISITION

/usr/delta/global/experiments/std_acquisition--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_acquisition---- Standard Experiment Acquisition include file--filter_width = x_sweep/2;x_acq_time =? x_points/x_sweep;x_resolution =? 1/x_acq_time;

STD_2D_ACQUISITION

/usr/delta/global/experiments/std_2d_acquisition--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_2d_acquisition---- Standard Experiment 2D Acquisition include file--y_acq_time =? y_points/y_sweep;y_resolution =? 1/y_acq_time;

A-2 DELTA User’s Guide, v 3.2

STD_3D_ACQUISITION

/usr/delta/global/experiments/std_3d_acquistion--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_3d_acquisition---- Standard Experiment 2D Acquisition include file--z_acq_time =? z_points/z_sweep;z_resolution =? 1/z_acq_time;

SET_DEC_INSTRUMENT

/usr/delta/global/experiments/std_dec_instrument--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_instrument---- Standard Experiment Instrument include file--solvent => #;filter_mode = “BUTTERWORTH”;recvr_gain => 15;irr_noise => “WALTZ”;tri_noise = “WALTZ”;

std_domains


STD_DOMAINS

/usr/delta/global/experiments/std_domains--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_domains-- domain offset sweepProton 5[ppm] 15[ppm]Deuterium 5[ppm] 15[ppm]Lithium7 0[ppm] 20[ppm]Boron11 0[ppm] 250[ppm]Carbon13 100[ppm] 250[ppm]Nitrogen15 0[ppm] 600[ppm]Oxygen17 0[ppm] 600[ppm]Fluorine19 0[ppm] 400[ppm]Aluminum27 0[ppm] 500[ppm]Silicon29 0[ppm] 500[ppm]Phosphorus31 0[ppm] 700[ppm]Rhodium103 0[ppm] 1000[ppm]Cadmium113 0[ppm] 800[ppm]Tin119 0[ppm] 1000[ppm]Xenon129 0[ppm] 1000[ppm]Tungsten183 0[ppm] 1000[ppm]Platinum195 0[ppm] 1000[ppm]Mercury199 0[ppm] 1000[ppm]Lead207 0[ppm] 1000[ppm]

STD_DOMAIND_MASTER_LIST

/usr/delta/global/experiments/std_domains_master_list--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ---------------------------------------------------------------------------------

This file is used only for reference when updating the std_domains file.


STD_HEADER

/usr/delta/global/experiments/std_header

--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ---------------------------------------------------------------------------------

-- std_header---- Standard Experiment Header include file----allow_copy = true;auto_dwell = true;--auto_filter = false;auto_gain => false;--automatic = false;--create_file = true;--comment = ““;--destination = ““;--eject = false;--filename = ““;--filter_limit = 0;--filter_start = 0.0;--filter_stop = 0.0;--filter_wide = false;force_tune => false;--force_vector = false;--hold = false;--init_group = 0;--job_group = false;--load_pulser = true;--load_shims = false;--lock_check = false;--match = true;--module_config = ““;--multi_file = false;--not_owned = false;--pre_post = true;--probe_attr = ““;--process = ““;--process_copy = true;--quick_tune = false;--repeat = false;--resubmit = false;--round_points = true;

std_instrument


--sample_id = ““;save_aborted = true;--sawtooth = false;--settle_vt = false;--slot = 0;--sn_border = 100;--sn_noise_start = 0.0;--sn_noise_stop = 0.0;--sn_ratio = 0;--sn_signal_start = 0.0;--sn_signal_stop = 0.0;--sn_skip = 10;--start_time = ““;vector = true;

STD_INSTRUMENT

/usr/delta/global/experiments/std_instrument--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_instrument---- Standard Experiment Instrument include file--solvent => #;filter_mode => “BUTTERWORTH”;recvr_gain => 15;irr_noise = “WALTZ”;tri_noise = “WALTZ”;

STD_PULSE

/usr/delta/global/experiments/std_pulse--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_pulse---- Standard Experiment Pulse include file-- macro acq ( dead_time, delay, phase ) is


dead_time, (reset); delay, (reset,rcv.gate); acquire (reset,rcv.phs.phase); end acq;

define dead_time = if not auto_dwell then if filter_mode = “BUTTERWORTH” then

if 0.6/x_sweep - x_pulse/2 < 15`[us] then 15`[us] else 0.6/x_sweep - x_pulse/2 else 20`[us] else 0`[us];

define delay = if not auto_dwell then if filter_mode = “BUTTERWORTH” then if 0.4/x_sweep < 0.5`[us] then 0.5`[us] else 0.4/x_sweep else 0.6/x_sweep else 0`[us];

define phase_preset = 2`[us];

STD_SOLID_INSTRUMENT

--------------------------------------------------------------------------------- ---- Experiment Source Code ---- Delta NMR Experiment & Machine Control Interface ---- ---- Copyright (c) 1996 JEOL USA, Inc. ---- All Rights Reserved ---- ----------------------------------------------------------------------------------- std_instrument---- Standard Experiment Instrument include file---- solvent => #;filter_mode = “BUTTERWORTH”;recvr_gain => 15;irr_noise = “WALTZ”;tri_noise = “WALTZ”;

DELTA User’s Guide, v3.2 B-1

APPENDIX B: INSTRUMENT PARAMETERS

This table lists the spectrometer machineparameters. For specific informationregarding these parameters, please contactJEOL applications.

A90A90_HIA90_LOADC_CARDAUTOLOCK_LEVELAUTOSHIM_DELAYAUTOSHIM_MODEAUTOSHIM_TRACKAUTOTUNE_DIAL_STATEB90B90_HIB90_LOBBUS_INTERFACE_IN_0BBUS_INTERFACE_IN_1BBUS_INTERFACE_IN_2BBUS_INTERFACE_IN_3BBUS_INTERFACE_OUT_0BBUS_INTERFACE_OUT_1BBUS_INTERFACE_OUT_2BBUS_INTERFACE_OUT_3C90C90_HIC90_LOCHANGER_SAMPLECHANGER_SAMPLE_UNLOADD90D90_HID90_LODEUT_GRAD_SHIM_90DEUT_GRAD_SHIM_ATTNE90E90_HIE90_LOEND_TIMEEXPERIMENTFACTORSFIELD_STRENGTH

FILTER_MODEFILTER_WIDTHHE_LEVELHF_MATCH_DIALHF_TUNE_DIALIRR90IRR90_HIIRR90_LOIRR_CODEIRR_NOISEIRR_PWIDTHITERATIONSLF_MATCH_DIALLF_TUNE_DIALLOCAL_TIMELOCK_ACHIEVE_POINTLOCK_GAINLOCK_LEVELLOCK_OSC_OFFSETLOCK_OSC_STATELOCK_PHASELOCK_SETTLE_POINTLOCK_STATELOCK_STATUSLOCK_STRENGTHN2_LEVELNUM_SCANSOBS_NOISEOBS_PWIDTHORDERSPASS_RIPPLEPROBE_ATNPROBE_COARSEPROBE_IDPROBE_MATCHPROBE_TUNEQUA90QUA90_HIQUA90_LOQUA_NOISEQUA_PWIDTHRECVR_GAINSAMPLE_ACTION

B-2 Delta User’s Guide, v3.2

SAMPLE_STATESAMPLE_STATUSSAWTOOTH_RANGESHIM_MAX_RECALLSHIM_NAMESSHIM_XSHIM_X2SHIM_X2ZSHIM_X2Z2SHIM_X2Z3SHIM_X2Z4SHIM_X3SHIM_X3ZSHIM_X3Z2SHIM_X3Z3SHIM_X4SHIM_X4ZSHIM_X4Z2SHIM_XZSHIM_XZ2SHIM_XZ3SHIM_XZ4SHIM_XZ5SHIM_YSHIM_Y2SHIM_Y2ZSHIM_Y2Z2SHIM_Y2Z3SHIM_Y2Z4SHIM_Y3SHIM_Y3ZSHIM_Y3Z2SHIM_Y3Z3SHIM_Y4SHIM_Y4ZSHIM_Y4Z2SHIM_YZSHIM_YZ2SHIM_YZ3SHIM_YZ4SHIM_YZ5SHIM_Z0SHIM_Z1SHIM_Z2SHIM_Z3SHIM_Z4

SHIM_Z5SHIM_Z6SHIM_Z7SHIM_Z8SOLVENTSPIN_ACTIONSPIN_GAS_SOURCESPIN_GETSPIN_LOCK_90SPIN_LOCK_ATTNSPIN_SETSPIN_STATESPIN_STATUSSTOP_RIPPLETEMP_ACTIONTEMP_AMBIENTTEMP_BOILINGTEMP_COMPTEMP_DELAYTEMP_GETTEMP_LIMIT_HITEMP_LIMIT_HI_MAXTEMP_LIMIT_HI_MINTEMP_LIMIT_LOTEMP_LIMIT_LO_MINTEMP_LIMIT_MD_MAXTEMP_LIMIT_MD_MINTEMP_MELTINGTEMP_RAMP_STEPTEMP_RAMP_WAITTEMP_SETTEMP_STATETEMP_STATUSTRANSITION_RATIOTRI90TRI90_HITRI90_LOTRI_NOISETRI_PWIDTHVT_PID_LONG_0_H_CBHVT_PID_LONG_0_H_CBLVT_PID_LONG_0_H_HCVT_PID_LONG_0_H_HLVT_PID_LONG_0_H_PBVT_PID_LONG_0_H_TDVT_PID_LONG_0_H_TI

Delta User’s Guide, v3.2 B-3

VT_PID_LONG_0_M_CBHVT_PID_LONG_0_M_CBLVT_PID_LONG_0_M_HCVT_PID_LONG_0_M_HLVT_PID_LONG_0_M_PBVT_PID_LONG_0_M_TDVT_PID_LONG_0_M_TIVT_PID_LONG_40_H_CBHVT_PID_LONG_40_H_CBLVT_PID_LONG_40_H_HCVT_PID_LONG_40_H_HLVT_PID_LONG_40_H_PBVT_PID_LONG_40_H_TDVT_PID_LONG_40_H_TIVT_PID_LONG_40_M_CBHVT_PID_LONG_40_M_CBLVT_PID_LONG_40_M_HCVT_PID_LONG_40_M_HLVT_PID_LONG_40_M_PBVT_PID_LONG_40_M_TDVT_PID_LONG_40_M_TIVT_PID_STD_NB_H_CBHVT_PID_STD_NB_H_CBLVT_PID_STD_NB_H_HCVT_PID_STD_NB_H_HLVT_PID_STD_NB_H_PBVT_PID_STD_NB_H_TDVT_PID_STD_NB_H_TIVT_PID_STD_NB_L_CBHVT_PID_STD_NB_L_CBLVT_PID_STD_NB_L_HCVT_PID_STD_NB_L_HLVT_PID_STD_NB_L_PBVT_PID_STD_NB_L_TDVT_PID_STD_NB_L_TIVT_PID_STD_NB_M_CBHVT_PID_STD_NB_M_CBLVT_PID_STD_NB_M_HCVT_PID_STD_NB_M_HLVT_PID_STD_NB_M_PBVT_PID_STD_NB_M_TDVT_PID_STD_NB_M_TIVT_PID_STD_WB_H_CBHVT_PID_STD_WB_H_CBLVT_PID_STD_WB_H_HCVT_PID_STD_WB_H_HL

VT_PID_STD_WB_H_PBVT_PID_STD_WB_H_TDVT_PID_STD_WB_H_TIVT_PID_STD_WB_L_CBHVT_PID_STD_WB_L_CBLVT_PID_STD_WB_L_HCVT_PID_STD_WB_L_HLVT_PID_STD_WB_L_PBVT_PID_STD_WB_L_TDVT_PID_STD_WB_L_TIVT_PID_STD_WB_M_CBHVT_PID_STD_WB_M_CBLVT_PID_STD_WB_M_HCVT_PID_STD_WB_M_HLVT_PID_STD_WB_M_PBVT_PID_STD_WB_M_TDVT_PID_STD_WB_M_TIX90X90_HIX90_LOY90Y90_HIY90_LOZ90Z90_HIZ90_LO

B-4 Delta User’s Guide, v3.2

DELTA User’s Guide, v 3.2 C-1

APPENDIX C: IRRADIATION CODES

The irr_codes are the base 10 representation of the octal number determined by thetable below.

This chart gives the octal number, not the actual Eclipse irr_code. For example, theTH5 probe requires a 9 watt high power pulse and 1.5 watts of decoupling for both non-acquisition and acquisition times. Therefore the bit settings are as follows:

To convert the octal value to decimal (base 10):2228 = 2*(64) + 2*(8) + 2*(1) = 14610

Thus the correct irr_code for the TH5 probe is 146.

The high power decoupler pulses are active only when the correct feature is activated inthe module_config line.

For GX, GSX, and CPF spectrometers retrofitted with a Delta Upgrade, onlytwo irr_codes are valid (only the lowest 3 bits are read). Therefore, anirr_code <= 4 will deliver the “4 watt” level and an irr_code >= 5will deliver the “9 watt” level.

Table 10-1: Irradiation Codes

high powerdecoupler level

non-acquisition level acquisition level

bits 7 6 5 4 3 3 2 1

0 0 2watt 0 0 0 0.5 watt 0 0 0 0.5 watt

0 1 4 watt 0 0 1 1.0 watt 0 0 1 1.0 watt

1 0 9 watt 0 1 0 1.5 watt 0 1 0 1.5 watt

1 1 full power 0 1 1 2.0 watt 0 1 1 2.0 watt

1 0 0 4.0 watt 1 0 0 4.0 watt

1 0 1 9.0 watt 1 0 1 9.0 watt

Table 10-2: Conversion Example for TH5 Probe

bits 7 6 5 4 3 2 1 0

binary 1 0 0 1 0 0 1 0

octal 2 2 2

C-2 DELTA User’s Guide, v 3.2

DELTA User’s Guide, v 3.2 D-1

APPENDIX D: DECOUPLING ON A GX, GSX, OR CPF

DELTA UPGRADE SPECTROMETER

The amplifier control unit in the GX, GSX, and CPF spectrometers is much more limitedthan the EX (Eclipse) spectrometer.

For all GX, GSX, and CPF Delta upgrades, verify the GSX_COMPAT flag inthe machine.config file is set TRUE and the comment characters (--) areremoved.

This information is provided for reference use only. Because of the widevariety of ages of GX, GSX, and CPF instruments, and thus a variety ofPROMs in the amplifier control unit, any information given here must beverified with an RF power meter or oscilloscope before the Delta Upgrade iscompleted. Not all GX and GSX spectrometers are equipped to do all theexperiments listed herein.

The user is urged to read and understand all of the material before makingmodifications to any experiments. If a user has any doubts about makingchanges to an experiment, please contact either the JEOL NMR Applicationsdepartment or the JEOL NMR Service department prior to making themodifications.

PROTON DECOUPLING FROM EITHER IRR OR TRR CHANNEL

The GX amplifier control unit supports only two power levels, a nominal 4 watt and anominal 9 watt level. This is true for both decoupler channels with running 1H. Theirr_code control for these levels is:

If the system is to be used with current generation probes, we recommend reducing the “4watt” level to approximately 2 watts. With Waugh or Waltz decoupling, 2 watts willprovide more than sufficient bandwidth for normal use. If the system will be used witholder style probes, 4 watts may be necessary, however it is always best to reduce theamount of power.

Table D-1: GX Decoupler Amplifier Control

irr_code power level att&sum adjustment

less than or equal to 4 “4 watt” level VR6

greater than or equal to 5 “9 watt” level VR7

D-2 DELTA User’s Guide, v 3.2

HIGH POWER 1H DECOUPLER SEQUENCES FROM EITHER IRR OR TRRCHANNEL

“High power” decoupler sequences are those that used an IRAPC value of 100 or greaterin the PEGS pulse program. In that mode the amplifiers delivered a full RF power to theprobe. This mode corresponds to the amp_full_pwr in the Delta pulse language.

On GX and GSX spectrometers, no facility exists for automatically reducing thedecoupler power during the acquisition. Thus, a separate attenuator line must be used to

reduce the RF power during the acquisition if broadband 1H decoupling is used.

Do not run a “high power” sequence until the power levels and attenuator aremeasured with a power meter.

Failure to observe this important difference will result in damage to yourprobe. If you plan to use “high power decoupler” sequences, take specialprecaution to determine the power levels in a dummy RF load first.

The user is urged to read and understand all of the material before makingmodifications to any experiments. If a user has any doubts about makingchanges to an experiment, please contact either the JEOL NMR Applicationsdepartment or the JEOL NMR Service department prior to making themodifications.

BILEVEL 1H DECOUPLING

Bilevel control is done on both the GSX and EX systems with the PEGS bit 7. Bit 7 iscalled rf_limit in the Eclipse experiments. When the machine_config bileveloption is enabled, and the rf_limit gate is ON, the 1H decoupler RF level is set toACQTM level on EX and “9 watt” level on GSX. When the rf_limit is OFF, thedecoupler power is NON-ACQ on the EX and “4 watt” on the GSX.

On a GX, GSX or CPF, if the irr_code = 4 (“4 watt” level), then the bilevel bit willhave no effect, if the irr_code = 7 (“9 watt” level) for a probe, then the bilevel bitwill allow the rf_limit bit to become active.

On the GX, GSX or CPF spectrometers, to get bilevel control below the “4 watt” level, thenormal oscillator attenuators must be used and a special GSX experiment is required.

LOW FREQUENCY (X-NUCLEUS) DECOUPLING FROM THE TRR CHANNEL

This section describes certain features and options of the spectrometer that,when used incorrectly, could damage certain NMR probes. The user is urged toread and understand all of the material before making modifications to anyexperiments. If a user has any doubts about making changes to an experiment,please contact either the JEOL NMR Applications department or the JEOL

Low frequency (X-nucleus) decoupling from the TRR channel

DELTA User’s Guide, v 3.2 D-3

NMR Service department prior to making the modifications.This section is applicable ONLY to GX, GSX or CPF systems that aremodified to do reverse detection or X-nucleus decoupling experiments. If youare not sure about your system, contact the JEOL NMR Service department.

If the spectrometer is modified and equipped to do reverse detection, the power levelsfrom the TRR (X channel) must be verified. The IRR channel is capable of running only1H, however the TRR channel can accept any oscillator.

A major difference exists with the LF channel. Depending on the PROM, rf_limit maywork on the TRR channel when generating LF frequencies. This must be verified on eachinstrument that does X-nucleus decoupling.

Set the LF decoupler power with the rf_limit level with VR2 on the att&sum unit.

D-4 DELTA User’s Guide, v 3.2

DELTA User’s Guide, v 3.2 E-1

APPENDIX E: DIRECTORIES AND FILES USED BY DELTA

This appendix describes the directories and files used by the Delta NMR processingsoftware and the Eclipse NMR spectrometer. The major divisions are the user account, thesystem Delta directories, and the Eclipse spectrometer directories.

DELTA USER ACCOUNT

Delta is the normal login account for users.

❏ ./delta/This the top directory for user-specific files. These directories are created by the defaultcopy_setup script file and are used as the initial default locations for file requests bythe user or a Delta program.

./delta/library/This is the default user directory which contains the user’s function library. Itcontains the compiled Percival programs, the local Percival operators (.l files), andthe local_percival_operator_library.1 file. This directory isdeclared by the LIBRARY flag in the .delta_configure file.

./delta/p_files/This is the default user directory which contains the source for user Percivalprograms and operators. This directory is declared by the SOURCE flag in the.delta_configure file.

./delta/process_lists/This is the default user directory which contains the processing lists for theprocess_oned and process_nd tools and the process_local_listoperator. This directory is declared by the PROCESS_LIST flag in the.delta_configure file.

./delta/templates/This is the default user directory which contains user-defined templates for tools thatneed them (2DViewer, 3DViewer, etc.) -- plotter layout templates for the plot tooland user templates for data_slate displays. This directory is declared by theTEMPLATE flag in the .delta_configure file.

./delta/experiments/This is the default user directory which contains the local user-written experimentsfor the Eclipse NMR Spectrometer. This directory is declared by the EXPERIMENTflag in the .delta_configure file.

./delta/instrument/This is the default user directory which contains the user Shim files and other relateduser instrument files. This directory is declared by the INSTRUMENT flag in the.delta_configure file.

E-2 DELTA User’s Guide, v 3.2

./delta/reports/This is the default user directory which contains the user-produced reports generatedby Delta, including plots to files, output from the peak spreadsheet database, orreports from Percival programs or functions. This directory is declared by theREPORT_OUTPUT flag in the .delta_configure file.

❏ ./.icons/This directory contains the user-specific icons used by the IRIX operating system on theSilicon Graphics workstation.

Delta.iconThis file contains the icon used when Delta windows are iconified.

login.iconThis file contains the icon used for the Delta user account on the Pandora display.Pandora is the display containing user icons when no one is logged in to the SiliconGraphics workstation. This file can be changed to reflect the user's artistic taste.

❏ ./files/This directory contains the directories which contain unconverted user data and data in theDelta format. These directories are created by the default copy_setup script file andare used as the initial default data locations.

./files/data/This directory contains user Delta data, and is declared by the DATA flag in the.delta_configure file. Eclipse data is uploaded to this directory from theEclipse NMR Spectrometer.

./files/foreign_data/This directory contains data in foreign formats (not collected on a JEOLspectrometer) that must be converted to the Delta format before processing anddisplay. The data located here are typically JEOL GX/GSX/CPF/EX data, JEOLAlpha data, and other non-Delta data formats.

The format converters use this directory as the default location for foreign datatypes. The GX, GSX, CPF, EX, Alpha, Varian VNMR, Bruker Aspect, and otherNMR data files would be located in this directory and converted to Delta data.

Delta System Directories, /usr/delta/


DELTA SYSTEM DIRECTORIES, /USR/DELTA/

This is the set of directories that contain the Delta programs and system default files for allDelta users.

/USR/DELTA/GLOBAL/ FILES

This directory contains the Delta executable UNIX programs, the compiled Delta Percivalprograms and operators, and the assignment label files. Normally this is /usr/delta/global/, but Delta may be installed in a different location.

❏ .delta_product_keyThis file contains the workstation specific software key to allow Delta to run on aparticular workstation. One entry in this file is required for each workstation that will usethe Delta software from this directory. This file can be appended to or created by the verifyprogram.

Sample .delta_product_key file:AT-RW-RM-3O-HX -- Delta

❏ consoleThis program is an auxiliary console for Delta. It uses the message manager to talk toDelta running on the local workstation. It functions like the input box option on the Deltaconsole.

Help output from the console program:/usr/delta/global/console [-r -l -e -s number] -r : Reset all client ids -l : List all available servers -s : Select a server by number -e : Line editor enabled (Default) -w : Without line editor enabled -p : Initial prompt mode -n : Tell Delta which server daemon should respond to this console. -h : Connect to host.

Switches:-r Resets all message ID's used to manage message passing.-l Lists all of the copies of Delta running on a system.-s Selects a specific Delta program with which to communicate.-e Enables a line editor similar to the one on the Delta Console.-w Works without line editor enabled.-p Is the initial prompt mode.-n Tells Delta which server daemon should respond to this console.-h Connects to the host.

❏ deltaThis is the Delta program, by default this program executes the delta_startup.1Percival program at runtime.


Help output from the delta program:usage : /usr/delta/global/delta [-hvnliwgmrs filename][-f info]Copyright 1996 JEOL USA, Inc -g : Disable Window Manager Graphics -h : Display Help -i : Disable Instrument Manager -l : Enable Local Console -n : Do Not Start -r : reset all message ids -v : Display Version -w : Disable Window Manager -x : Use mixed mode graphics (X11/OpenGL geometries) -f : Specify input info -s : Specify startup file --ogl : Force use of OpenGL graphics --igl : Force use of IRISGL graphics --x11 : Force use of X11 graphics --single : Force single-buffering --sync : Force synchonization with X server

Switches:-g Prevents Delta from drawing to the screen, but allows Delta to generate data plots.

Currently works only on SGI servers.-h Prints the switch help information listed above.-i Prevents Delta from connecting to active instruments by disabling the instrument

manager.-l Creates a local console to allow commands to be entered from the Percival prompt.

This is similar to the yellow input box option found on the Delta Console.-n Causes Delta to load execute any other switches, typically -h or -v, and to

terminate execution.-r Resets all message ID's, used to manage message passing.-v Prints the version information for Delta, program execution continues after

printing. The version flag will also designate other available options, the softwareserial number, and the machine’s ID.

-w Prevents Delta from doing any graphics, data plotting included.-x Uses mixed mode graphics. Use X11 for everything except geometries.-f Allows a Delta program to be started and data passed into Delta for execution at

startup.-s Allows an alternate Percival startup file to be executed at beginning of the Delta

program execution.--ogl Forces use of OpenGL graphics.--igl Forces use of IRISGL graphics.--x11 Force use of X11 graphics.--singl Force single-buffering for graphics.--sync Force synchronization of the X server.

/usr/delta/global/ Files


❏ jdcThe JEOL Delta Compiler, jdc is used to compile Percival programs and operators. Theinput files are Percival Source (*.p) files, and the output files are Percival executable(*.1) files.

Help output from the jdc program:usage : /usr/delta/global/jdc [-swqmnreldg] file1 file2 ...Copyright 1996 JEOL USA, Inc

-s : Show compiling statistics -w : display warnings -q : Suppress all titles and output except errors -m : Display machine code -n : Suppress symbol tables -r : Recompile the specified files in place -e : Extract the source code for specified executables -l : List operators in library -d : Delete operators from library -g : Global library flag

if extension is omitted from filenames, '.p' is assumed.

Switches:-s Displays the number of Percival lines compiled and the compiler speed in number of

lines compiled per second.-w Displays all Percival compile time warnings. Normally these are suppressed, and

appear only when a compile error is encountered in a Percival source file.-q Stops the printing of normal output except for errors encountered.-m Displays the P code that jdc generates when compiling a Percival source file. This

P code is the code that Delta interprets for Percival program execution.-n Suppresses the symbol table for Percival programs. This saves on memory and

loading time. The symbol tables are used for debugging Percival code.-r Recompiles a Percival program or operator to update the pointers to other Percival

operators that may have changed.-e Extracts a Percival operator and creates a Percival source file.-l Lists the operators in both the local and the global Percival operator libraries.-d Deletes an operator from either the local or the global Percival operator library.-g Directs the results of jdc operations to the /usr/delta/global/ directory.

❏ send_messageThis program sends a message to a running copy of Delta running on the same system. Ituses the message manager to talk to Delta running on the local workstation. The messagecan be a file name, or a program for Delta to run. Delta must be set up in advance tointerpret the message.

Help output from the send_message program:./send_message [-r] [-l] [-n name] [-s number] [-f command] [message] -r : Reset all client ids -l : List all available servers -s : Select a server by number


-n : Name of message -f : Command executed if no server found

Switches:-r Resets all message ID's and is used to manage message passing.-l Lists all copies of Delta running on a system.-s Selects a specific Delta program with which to communicate.-n Defines the name of the message for Delta operators to use.-f Defines the command to be executed if Delta is not running.

❏ nsend_messageThis program sends a message to a copy of Delta running on a remote system. It uses themessage manager to talk to Delta running on the local workstation. The message can be afile name, or a program for Delta to run. Delta must be set up in advance to interpret themessage.

Help output from the nsend_message program:./nsend_message nodename [-n name] [message] -n : Name of message

Switches:-n Defines the name of the message for Delta operators to use.

❏ verifyThis program generates and verifies the .delta_product_key file in the /usr/delta/global/ directory.

Help output from the verify program:verify [-h|-v|[-m]{Product-License-Key}]

License management tool : -h Print this message -m Causes a license key file to be created/appended -q Don’t print, just set status code -v Verify Product License Key file

Switches:-h Displays the help message.-m Creates a new .delta_product_key file or appends a new key to an existing

file.-q Don’t print, just set status code.-v Verifies entries in the .delta_product_key file.



❏ uploadThis Bourne shell script is used to automatically upload files to a Delta workstation fromthe Eclipse spectrometer when an experiment is finished.

Sample upload script file:#! /bin/shPATH=/usr/bsd:/usr/sbin:/sbin:/bin:/usr/bin:/etcif [ $# -ne 3 ]; then echo “usage : $0 system targetfile destinationfile” echo “invoked as $0 $*” exit 1fi

hostname=`hostname`directory=`dirname “$3”`

if [ ! -d “$directory” ]; then mkdir -p “$directory”ficd “$directory”result=$?if [ $result -ne 0 ]; then echo “<3>upload[$$]: unable to cd to $directory” >/dev/log exit $resultfi

output=`ftp -n $1 2>&1 <<-! | head -1user anonymous ${hostname}@binaryget $2 upload$$!`test -z “$output”result=$?if [ $result -ne 0 ]; then echo “<3>upload[$$]: upload of $3 FAILED : $output” >/dev/log exit $resultfimv -f upload$$ `basename “$3”`result=$?if [ $result -ne 0 ]; then

echo “<4>upload[$$]: rename of $directory/upload$$ to $3FAILED” >/dev/logelse echo “<6>upload[$$]: upload of $3 succeeded” >/dev/logfiexit $result

❏ global_percival_operator_library.1This is the global library file for compiled Percival operators. Additions and deletions tothis library are controlled by the -g option on the JEOL Delta Compiler, jdc.

❏ *.1 filesThese files are the compiled Percival programs that Delta uses for execution. Percivalprograms are placed in the /usr/delta/global/ directory when the -g switch isused.


❏ assignment.* filesThe files, assignment.groups, assignment.residues, andassignment.types are used as the labels in the spreadsheet, and on plots. Do notchange the text in these files! Your assignments will not be correct if the body of these filesis changed after assignments have been made. You can make additions to the end of thesefiles if additional assignment labels are required. Characters preceded by a ^ are convertedto Greek.

❏ Data File Programs and Format ConvertersThese programs are used to convert, to export, to list information about, and to fixdamaged Delta data files.

❏ convertThis program is the standard data format converter for JEOL's GX, GSX, CPF, andEX NMR data files. This program will automatically convert 1D NMR data and 2Dcomplex by real data without any switches. It will also convert 2D complex by (real,complex or tppi) data, and 3D complex by (real, complex or tppi) by (real, complexor tppi) data when the appropriate switches, described below, are used. To redirectthe output to a file with a name different from the standard name use the -o switch.This must be the last switch and be immediately followed by the new filename andthe truncated *.gx* filename.

Converter Help: convertconvert [global_switches] -intype {inswitch}+ -outtype

{outswitch}+

Convert v1.10 Copyright (C) 1997-1998 JEOL libRX 1.5 Copyright (C) 1995, 1996 Tom Lord

This program is supported at following data format:

Import Vendor Product Input Max dimension -------------------------------------------------------------------------------------- JEOL GX FID 2 JEOL GSX FID 2 JEOL CPF FID 2 JEOL EX FID 2 JEOL ALPHA FID 4 JEOL Lambda FID 3 JEOL Alice FID 2 JEOL Eclipse/ECP/Delta FID/Spectrum 6 JEOL JEOL Generic FID/Spectrum 6 JEOL CMX FID 2 Varian INFINITY FID 2 Varian VXR FID 3



Varian UNITY FID 3 Bruker AC FID 3 Bruker AMX/DMX FID 3 Acorn NMR NUTSF ID/Spectrum 2 Galactic Grams/3 FID/Spectrum 2 MSI Felix FID/Spectrum 3 --- JCAMP-DX 5.0 FID/Spectrum 3

Export Vendor Product Output Max dimension ----------------------------------------------------------------------------------- JEOL GX FID 2 JEOL Alice FID 2 JEOL Eclipse/ECP/Delta FID/Spectrum 6 JEOL Generic FID/Spectrum 6 AcornNMR NUTS FID/Spectrum 2 Galactic Grams/32 FID/Spectrum 2 MSI Felix FID 3

NMR Pipe FID 3JCAMP-DX 5.0 FID/Spectrum 3

Usage convert [global_switch] -intype {inswitch} -outtype {outswitch}

global_switch : -help [intype outtype] : display help -server [serverID] : information server ID -quiet : quiet mode (no message display)

intype -delta : JEOL Eclipse/ECP/Delta -gx : JEOL GX/GSX/CPF/EX -alpha : JEOL ALPHA -lambda : JEOL Lambda -alice : JEOL Alice -jeol_generic : JEOL Generic format -cmx : JEOL CMX / Varian INFINITY -vxr_unity : Varian VXR/UNITY -ac : Bruker AC -amx : Bruker AMX/DMX -cdff_nuts : Acorn NMR NUTS -galactic : Galactic Grams -felix : MSI Felix -jcamp : JCAMP-DX 5.0 format

inswitch


-file [filename] : input file (or directory) name -separate : use JEOL GX/GSX/CPF/EX 2D phase sensitive data ..... others.(See help of intype)

outtype -delta : JEOL Eclipse/ECP/Delta -gx : JEOL GX/GSX/CPF/EX -alice : JEOL Alice -jeol_generic : JEOL Generic format -cmx : JEOL CMX / Varian INFINITY -cdff_nuts : Acorn NMR NUTS -galactic : Galactic Grams -felix : MSI Felix -nmrpipe : NMR Pipe -jcamp : JCAMP-DX 5.0 format

outswitch -file [filename]: output file name

Examples:

convert -alpha -file GLUCOSE_HSQC.NMF -delta -file glucose_hsqc

This command would convert from ALPHA’s file ’GLUCOSE_HSQC.NMF’ to ECP’sfile ’glucose_hsqc’.

Examples:

convert -Ra -Ib -ir -c2 -o gramacidin gram

This would convert the files 'grama.gxd' and 'gramb.gxd' into the file 'gramacidin'using the irradiation frequency as the observation frequency.

convert -c2 -c3 4 EXP

This would convert the files 'EXPRR1.GXD', 'EXPRI1.GXD', 'EXPIR1.GXD','EXPII1.GXD', 'EXPRR2.GXD', etc. into 'exp' using the observation frequency.

❏ fixupThis program will attempt to fix problems with the header of a Delta data file. Theseproblems sometimes occur when Delta crashes with files open.



❏ list_headerThis program will list the header sections of a Delta data file.

Help output from the list_header program:/usr/delta/global/list_header : [-+][acfhlp] files...Use - (+) to turn off (on) annotations, condensed format, full header, history, lists, parametersUse - (+) alone to turn off (on) all

Switches:+ Lists all sections or a particular listing when used with one of the switches below.- Prevents all or a particular section from being listed.a Lists any annotations present in the data set.c Lists all dimensional information on a single line.f Lists the full header information.h Lists the processing history of the file.l Lists the non-ranged lists in the file header, for example t1 value lists.p Lists acquisition parameters.

❏ Icons & LogosThese files are icons and logos used by Delta for Percival tools and plots.

❏ delta_screen.rgbThis file is displayed on a system before the demo license key expires and does not havea valid .delta_product_key file.

❏ global.rgbThis file is used as a push button in the standard file selection window. It initially selectsa global directory for the file type being opened or saved.

❏ jeol.epsThis file is used as a logo on plots. It is an Encapsulated Postscript (EPS). You maymake your own logo with a standard word processor by printing to an EPS file andcopying it to /usr/delta/global/ with the filename jeol.eps. This logowill appear only on postscript printers.

❏ local.rgbThis file is used as a pushbutton in the standard file selection window. It initially selectsa local directory for the file type being opened or saved.


❏ spinning_delta#.RGB infoThese files make up the Delta icon with the JEOL USA logo.

❏ ding.aifc This is the default sound file the bell operator will play.

/usr/delta/global/ Directories


/USR/DELTA/GLOBAL/ DIRECTORIES

❏ /usr/delta/global/automation/This directory contains files required for automation. This directory will be omitted orempty if Delta was installed without machine control.

❏ usr/delta/global/experiments/This directory and its sub-directories contain the standard JEOL-supplied experimentsthat are globally accessible to all users. This is the initial directory for JEOL-suppliedglobal experiments. This directory is will be omitted or empty if Delta was installedwithout machine control.

❏ /usr/delta/global/help/This directory contains the files used for the JEOL Delta Help system.

*.html FilesThese files form the JEOL Delta Help system.

*.gif FilesImage files for the JEOL Delta Help system.

❏ usr/delta/global/process_lists/This directory contains standard processing lists that are globally accessible to allusers. The standard automation also uses some of the lists for data processing.

❏ usr/delta/global/templates/This directory contains viewer, automation, and plotter layout templates that areglobally accessible to all users.

❏ *.pmtThese types of files are Presentation Manager templates.

❏ *.epsThese types of files are encapsulated Postscript files for the Presentation Manager.

❏ *.autoThese types of files are Automation templates.

❏ .delta_automation.autoThe default JEOL supplied Automation template. This file contains many commonlyused experiments.


/USR/DELTA/SETUP/

This directory contains the standard files used by the Delta user account, the printers, andother system configuration files for Delta. Files beginning with dot.filename arerenamed .filename and do not appear in standard file listings, such as ls -l.

❏ copy_setup script fileThis shell script will create the standard Delta user directories, and copy standard UNIXconfiguration files to the user's root directory. Warning: this script overwrites existingfiles in the user’s directories.

Files for USER Setup:

❏ Delta.iconThis file contains the icon used when Delta windows are iconified. It is copied to the.icons/ directory.

❏ .auxchestrcThis file contains descriptions for the toolchest found in the upper left of the screen.For more information, type man toolchest in an X terminal shell window.

❏ .cshrcThis is a file used by the shell that sets UNIX environment variables and creates astandard set of aliases for Delta. Aliases are convenient shortcuts for using Delta andfor navigating between the directories that Delta uses. This file is run each time anxwsh terminal window is created. The aliases generated by this file can be viewedby typing alias in an X terminal shell window.

❏ .delta_configureThis file is the standard Delta configuration file. It is described in detail in the DeltaUser Account Section.

❏ delta_dropCopy and rename this command to the name of a Delta tool (such as data_slate)and place it’s icon on the desktop. You can then bring up the tool by dropping adata file on it. Delta will start if it is not running.

❏ .delta_parameter_listThis file is the standard Delta parameter list file. It contains user-selected parametersthat appear in the parameter list tool and on parameter plots.

❏ .grosviewThis file contains configuration information for gr_osview, a system usagemonitoring tool. The gr_osview program can be started by typing gr_osviewin an X terminal shell window, or by selecting the system usage button in thetoolchest.

/usr/delta/setup/


❏ .loginThis file is run when the user logs in. The .login file sets the search path foruser-entered commands, and sets the environment variables used by UNIX.

❏ .icons/login.iconThis file contains the icon used for the Delta user account on the Pandora display.Pandora is the display containing user icons when no one is logged into the SiliconGraphics workstation. This file can be changed to reflect the user's artistic taste.

❏ pullThis file is a shell script used to move files from a JEOL GX/GSX/CPF/EX datasystem to the SGI system. The PDP system needs to have ftp running on it.

❏ copy_setupCopies the Delta setup and configuration files to the user’s login accountdirectories. Use caution. This will remove the user’s current login settings.

❏ .delta_configure_rootThis file is similar in structure to the .delta_configure file, but is only usedby the root account.

❏ get_spectrometersPrints out a list of spectrometers available on the network.

❏ kermitKermit is used with the shim robot. This is copy of kermit-C from ColumbiaUniversity. All rights are reserved, and this copy of kermit is being supplied atno charge.

❏ X keyboard filesThese files used for X Windows emulators:

❏ exceed_delta.kbf & wrq_delta.dmpKeyboard mapping files for PC computers running Exceed or Reflections (XWindows server applications) under Microsoft Windows (r).

❏ exodus_delta.binKeyboard mapping files for Macintosh computers running Exodus, an X Windowsserver application.


DELTA PERCIVAL SOURCE FILES

❏ /usr/delta/source/This directory contains the source for the JEOL supplied Percival programs andoperators.

*.p FilesThese files contain the standard Delta Percival source code for the Percival programsand operators used by Delta.

ECLIPSE FILES FOR ACQUISITION SYSTEM

❏ /usr/delta/eclipse/This directory contains the programs and configuration files used on the Eclipse NMRSpectrometer and on Delta-Upgrade systems. This directory will be omitted or emptyif Delta was installed without machine control.

backup_spectrometerThis script file is used to backup the Eclipse Acquisition system configuration filesfrom the acquisition system to the workstation.

restore_spectrometerThis script file is used to restore the Eclipse Acquisition system configuration filesfrom the workstation to the acquisition system.

update_spectrometerThis script file is used to update the Eclipse program files on a SGI V35 basedEclipse acquisition system running a version of SGI IRIX.

❏ /usr/delta/eclipse/probes/This directory contains the initial probe configuration files for the Eclipse NMRprobes.

❏ usr/delta/eclipse/dist/This directory contains Irix install files for SGI Indy based acquisition systemsRunning Irix V5.3 or higher.

Delta Configuration Files


DELTA CONFIGURATION FILES

.delta_configureThis is the primary configuration file containing parameters to adjust the behavior of theDelta user environment. This file must reside in the user's root directory. The selections inthe .delta_configure file are managed by the Delta Console Preferences Tool.

This file must be in the root (login) directory for the user account. Entries that begin with“--” are comments and are not used as configuration parameters for Delta. Each entrymust be on one line. The “~” appearing in a preference entry will be substituted with theuser's root directory path name.

.delta_configure File Entries for the Preferences Tool:

Note: entries that have a * require Delta to be restarted to be operative. Notealso that this list is alphabetized by the Preference Tool page, and that thename as it appears on the page is first, followed by the name that appears in the.delta_configure file, and when you select this title with the mouse.


❏ Personal Page:

Author, AUTHORThe name used by the Delta software and stored in data files collected by the user.This name designates the creator of the experiment data files. The default is“Delta Account”.

Browser, BROWSERThe full path (i.e. /usr/bin/netscape/) of the html browser used for help. Leaveblank unless help complains it cannot find Netscape.

Editor, EDITORThe Unix command used to invoke a text editor to use for editing files. If this entrydoes not exist, or does not refer to an existing program, then the PercivalCM~EDIT command will not function. The default is "/usr/sbin/jot", astandard editor supplied by Silicon Graphics.

Email, EMAILThe E-mail address of the author.

Instrument, DEFAULT_INSTRUMENTThe internet address of the spectrometer to auto-connect to when theSpectrometer Control Tool is opened. There is no default for this parameter.

Password, PASSWORDA password used for connecting to an Eclipse NMR spectrometer as the console. Ifthis password matches the password in the .delta_configure file on theEclipse Acquisition computer, the user is automatically connected as console. Ifthe password is supplied on the Spectrometer Control Tool, then the user willbe connected in Console Mode when the Connect button is pressed. There is not adefault password.

Site, SITEThis could be the name of a company or organization. There is no default for thisparameter.

Startup Console, DELTA_CONSOLE *The name(s) of a Percival program(s) that will be run when Delta is started.The default is "master_console".

Balloon Help, AUTO_HELP_ONON/OFF. When ON, and the mouse cursor is held still over a widget, for a certainamount of time, balloon help will appear automatically. The default is ON.

Balloon Help Delay, AUTO_HELP_TIMEThe number of seconds to wait over a widget before balloon help automatically



pops up. The default wait time is 1[s] (1 second).Balloon Help Time, HELP_WAIT_TIME

The number of seconds automatic pop-up help is visible. Setting this value to zerowill make balloon help visible as long as the mouse is over the widget. The defaultwait time is 1[s] (1 second).

Button Press Freq., STILL_PRESSED_TIMEThe time (in seconds) when a mouse button is held for a Percival message to besent that informs Delta that the mouse button is still pressed. The default is0.1[s] (1/10 second).

Double Click Rate, DOUBLE_CLICK_TIMEThe maximum length of time (in seconds) allowed to pass in which two mouseclicks must occur to constitute a double click. The default is 0.5[s] (1/2second).

Drag Delay, DRAG_WAIT_TIMEThe number of seconds to wait over a widget with the third mouse button pressedbefore the drag-and-drop dragon disappears. When the third mouse button ispressed, the mouse cursor changes to the Drag-and-Drop icon. The defaults is0.5[s] (1/2 second).

Confirmation, CONFIRMATIONON/OFF. When ON, the user is prompted for confirmation before certainpotentially harmful actions. The default is ON.

Simple Mode, SIMPLE_MODEON/OFF. A general parameter that is “global” to all tools with a simple mode ofoperation. The default is OFF.

❏ File/Directory Page:

Note: ~ in the directory paths indicate the user’s home directory.

Data, DATAThe directory (~/files/data/) containing user-generated Delta data, declaredby the DATA flag in the .delta_configure file. Eclipse data is uploaded tothis directory from the Eclipse NMR Spectrometer. It is the default local directoryfor Delta data files.

Executable, EXECUTABLEThe directory (~/delta/library/) for Percival executable files.

Experiment, EXPERIMENTThe directory (~/delta/experiments/) containing user-written experiments


for the Eclipse NMR Spectrometer. This directory is declared by the EXPERI-MENT flag in the .delta_configure file. It is the default local directory forDelta experiment files.

Foreign Data, FOREIGN_DATAThe foreign data directory (~/files/foreign_data/) containing data notcollected on a JEOL spectrometer that must be converted to the Delta formatbefore processing and display.

Gamma, GAMMAReserved for future use. The local directory for gamma files.

Global, GLOBALThe global directories containing the Delta executable UNIX programs and thecompiled Delta Percival programs and operators.

Warning! Do not change this value inside the Preferences Tool. It will

cause Delta’s internal operators to stop functioning properly.

Instrument, INSTRUMENTInstrument information directory (~/delta/instrument/) containing usershim files and other related user instrument files.

Library, LIBRARYThe library directory (~/delta/library/) specifying the location ofcompiled Percival operators (.l files) and the local library file.

PM Template, PM_TEMPLATEThe Presentation Manager directory. There is no default for this preference.

Process List, PROCESS_LISTThe directory (~/delta/process_lists/) specifying the location of theuser's process lists.

Report Output, REPORT_OUTPUTThe directory (~/delta/reports/) specifying the location for output.

Source, SOURCEThe directory (~/delta/p_files/) specifying the location of the user'sPercival programs (.p files).

Template, TEMPLATEThe directory (~/delta/templates/) specifying the location of templatesfor certain Delta tools.

Global Data, GLOBAL_DATA



The global directory where most of the Delta files exist.Global Executable, GLOBAL_EXECUTABLE.

The global directory for Percival executable programs.

Global Experiment, GLOBAL_EXPERIMENTThe global directory for experiment files.

Global Foreign Data, GLOBAL_FOREIGN_DATAThe global directory containing data in foreign formats (not collected on a JEOLspectrometer) that must be converted to the Delta format before processing anddisplay. The data located here are typically JEOL GX/GSX/CPF/EX data, JEOLAlpha data, and other non-Delta data formats.

Global Gamma, GLOBAL_GAMMAReserved for future use.

Global Instrument, GLOBAL_INSTRUMENTThe global directory containing user Shim files and other related user instrumentfiles. This directory is declared by the INSTRUMENT flag in the.delta_configure file.

Global Library, GLOBAL_LIBRARYThe global directory specifying the location of compiled Percival operators (.1files) and the local library file.

Global Process List, GLOBAL_PROCESS_LISTThe global directory specifying the location of the user's process lists.

Global Report Output, GLOBAL_REPORT_OUTPUTThe global directory specifying the location for reports. This is the defaultdirectory for Delta output files and messages.

Global Source, GLOBAL_SOURCEThe global directory specifying the location of the user's Percival source programs(.p files).

Global Template, GLOBAL_TEMPLATEThe global directory specifying the location of templates used for certain Deltatools.


❏ Printer/Plotter Page:

Printer, PRINTERThe name of the default printer (e.g. "lj4"). This printer is used by the printericon on many Delta tool bars. The name used must match the name found in theIRIX Print Manager Tool. There is no default for this preference.

Color Printer, PRINTER.COLORON/OFF. If ON, plots will be printed in color on color printers. This preferencehas no effect for BW printers. The default is OFF.

Printer Orientation, PRINTER.ORIENTATIONPORTRAIT/LANDSCAPE. Indicates the default plot orientation. The default isLANDSCAPE.

Printer Paper Size, PRINTER.PAPER_SIZEA/B/C/D/E/LEGAL/A0/A1/A2/A3/A4. A string that indicates the paper sizeloaded into the default printer. The default is A.

Peak/Integral Paper Size, PEAK_INTEGRAL_PAPER_SIZEA/B/C/D/E/LEGAL/A0/A1/A2/A3/A4. This value indicates paper size touse when printing peak and integral information. The default is A.

Printer Tessellate, PRINTER.TESSALATEAn integer between 1 and 64 that informs the printer of the number of triangles tobreak a surface into for plotting. The higher the number, the better the resolution ofthe data, but the more time it takes to compute. This value specifies the fineness ofpolygon size and color shading when plotting 2D or 3D spatial geometries. Lowernumbers create coarser shade differences, but are faster and require less memory.The defaults is 8.

Plot Options, PRINTER.OPTIONSCharacters that correspond to the features of a plotted geometry that effect thegeometry features that are displayed on the plot. There is no default for this param-eter.

Print JEOL Logo, PRINTER.JEOL_ICONON/OFF. If ON, then when data files are sent to be plotted, the JEOL icon (storedin jeol.eps) is plotted with the data. This determines whether the plot shouldinclude the JEOL icon. The default is OFF.

Print Parameters, PRINTER.PLOT_PARAMSON/OFF. When ON, the data file’s parameters are plotted with the data. Thedefault is OFF.

Parameters Location, PRINTER.LOCATION



LEFT/BOTTOM/RIGHT/TOP. Indicates where the data file parameters are toappear on data file plots. The default is LEFT.

Plot Border, PLOT_BORDERON/OFF. When ON, a thin border line is displayed around plots. The default isON.

Geometry: Negative Contour Grey, GEOMETRY.NEG_CONTOUR_GREYON/OFF. When ON, the negative peaks will be displayed in light gray (not black)when plotting a 2D contour. The default is ON.

Plot Dialog, PRINTER.DIALOGON/OFF. When printing from Process 1D or Data Slate and this preference isON, then a dialog box will appear allowing the user to set some printerconfiguration parameters before sending the plot to the printer. The dialog box willtime-out, and send the plot in 20 seconds if the printer parameters are not modified.The default is ON.

PostScript Emulator, PRINTER.POSTSCRIPT_EMULATORA boolean. Normally it is set to OFF, but if your printer is a PostScript emulatorand does not print PostScript files very well (long delays or errors duirng printing),then you may want to set this to ON.

Lines Per Page, PRINTER.LINES_PER_PAGEDefaults to FALSE. Can be any integer between 20 and 132. The numberof lines per page that the printer can print standard text files.

Plot Dash nWhere n = 1 - 8. When plotting overlaid data, each data set will be shown with thedash pattern specified. The pattern is used cyclically. Length of 1 is roughly 1millimeter.

❏ Data Page:

All Overlays, GEOMETRY_OPTIONS.ABR_FULLON/OFF. When ON, all overlays (file names and shadow dimensions) will bedisplayed in the upper left corner of a geometry. When OFF, only the filename andshadow dimension of the current slot is displayed. The default is OFF.

Annotations, GEOMETRY_OPTIONS.ANNOTATIONON/OFF. When ON, annotations will be visible on geometries. The default isON.

Comment, GEOMETRY_OPTIONS.COMMENTON/OFF. When ON, the file comment will be displayed in the upper left corner ofgeometries. The default is OFF.


Contour Line Check, LEVEL_TOOL.LINE_COUNT_CHECKON/OFF. When ON, the contour line limit will be checked when drawingcontours. When OFF, the limit is not checked and it may cause problems whencomputing contours below the peak threshold level. The default is ON.

Contour Line Limit, LEVEL_TOOL.LINE_COUNT_LIMITThe maximum number of line segments allowed to draw a contour line. If thenumber of line segments needed to draw a particular contour line exceeds thislimit, then the entire contour level will not be displayed. If Contour Line Check isset to OFF, this limit is not checked and may cause problems when computingcontours below the peak threshold level. The default is 5000.

Cursor, GEOMETRY_OPTIONS.CURSORON/OFF. When ON, geometry cursors are displayed on geometries and may becreated or destroyed. The default is OFF.

Data, GEOMETRY_OPTIONS.DATAON/OFF. When ON (the default), data is visible in the geometry. When OFF, thedata is hidden.

Data Points, GEOMETRY_OPTIONS.UNDERLINEON/OFF. For 1D files only. When ON, a small white square will be displayedaround each data point in the file. The default is OFF.

Deconvolve, GEOMETRY_OPTIONS.DECONVOLVEON/OFF. When ON, the primitive theoretical curves (deconvolutions) of the datapeaks displayed in geometries over the data if it has been computed. The default isOFF.

Deconvolve Sum, GEOMETRY_OPTIONS.DECONVOLVE_SUMON/OFF. When ON, the sum of the deconvolved peaks is displayed in geometriesover the data if the deconvolutions have been computed. The default is OFF.

Deconvolve Unselected, GEOMETRY_OPTIONS.DECONVOLVE_UNSELECTEDON/OFF. When OFF, the deconvolution curves are only displayed over the peakswhich are selected. Deconvolutions must be computed. The default is ON.

Draw: Backface, LEVEL_TOOL.BACKFACEON/OFF. When ON, the back faces of 3D and higher data sets are displayed.Otherwise, only data facing the viewer will be displayed. The default is ON.

Draw: Blend, LEVEL_TOOL.BLENDON/OFF. When ON, the pixels representing the data are displayed after blendingcolor with surrounding pixels. The result is a smoother, thicker data curve. Thedefault is ON.



Draw: Dither, LEVEL_TOOL.DITHERON/OFF. When ON, color is approximated with a dithering technique. The defaultis ON.

Draw: Double Side, LEVEL_TOOL.2SIDEON/OFF. When ON, both sides of the data are displayed. This will cause a see-through effect for 3D and higher data sets. The default is OFF.

Draw: Gradation, LEVEL_TOOL.GRADATIONON/OFF. When ON, the colors defined for Data Color are used for the contourcolors in 2D data sets. Otherwise, data color for the current slot value is used. Thedefault is OFF.

Draw: Smooth, LEVEL_TOOL.SMOOTHON/OFF. When ON, the data curve is smoothed with the anti-aliasing technique.The result is a less ragged data curve. The default is ON.

Draw: Solid, LEVEL_TOOL.SOLIDON/OFF. When ON, colors are displayed at full brightness for all levels. WhenOFF, colors are modified by the bias set in the Level Tool -- lower levels appeardimmed. The default is OFF.

Draw: Texture, LEVEL_TOOL.TEXTUREON/OFF. When ON, 2D and higher data sets when displayed in surface or meshmode will be displayed using the level colors. The default is OFF.

File Name, GEOMETRY_OPTIONS.INTEGERSON/OFF. When ON, the filename(s) of the data file(s) will be displayed in theupper left corner of geometries. The default is OFF.

Geom Border, GEOMETRY_OPTIONS.PLOT_GEOM_BORDERON/OFF. When ON, a thin border is displayed around geometries when plotted.The default is OFF.

Grid, GEOMETRY_OPTIONS.GRIDON/OFF. When ON, a grid will be displayed in the datazone area of geometries.The default is ON.

Integrals, GEOMETRY_OPTIONS.INTEGRATIONON/OFF. When ON, integrals will displayed over the data in geometries. Integralsmust be calculated or created. The default is OFF.

Integral Normal, INTEGRAL_NORMALThe value to which the largest integral will be normalized. The default is 1.

Integral Precision, INTEGRAL_PRECISION


The number of decimal points to display in the integral value(s). The default is 5.

Integral Tails, INTEGRAL_TAIL_MULTA multiplier indicating the desired length of the ends of integrals. A larger valuewill make the integral appear wider. The default is 1.

Integral Value, GEOMETRY_OPTIONS.INTEGRATION_VALUEON/OFF. When ON, integral values will be displayed next to the end of all integralcurves. The default is ON.

Line Hiding, GEOMETRY_OPTIONS.LINE_HIDINGON/OFF. For nD stack displays only. When OFF, all data vector lines aredisplayed completely. When ON, vectors in front in stack plots will occlude othervectors behind them, depending on the user's viewing angle. The default is OFF.

Note: Line hiding is computationally intensive and makes for much slowerrefresh drawing and refresh rates.

Peak, GEOMETRY_OPTIONS.PEAKON/OFF. When ON, peak positions will be displayed, and peaks can be createdand manipulated. Their axial positions will be indicated in the ruler or above thedata. The default is OFF.

Peak Above, GEOMETRY_OPTIONS.PEAK_ABOVEON/OFF. When ON, peak positions will be displayed above the peaks rather thanin the X ruler. Peak locations will marked by a white line above the peak in thedatazone area. The default is OFF.

Peak Integrals, GEOMETRY_OPTIONS.PEAK_INTEGRATIONON/OFF. When ON, integrals are displayed in grey for each peak, and can bemanipulated for peak groups. Integral information must exists in the data file forthe integrals to be visible. The default is OFF.

Peak Precision, PEAK_PRECISIONValues = 1..12. This is the number of decimal places to display for the peak pickvalues. The default = 5.

Max Peaks Allowed, MAX_PEAKS_ALLOWEDThe maximum number of peaks that will be found with the auto-analyze functionwhen an auto peak pick is performed. The default is 5000 peaks.

Plot Transparent, GEOMETRY_OPTIONS.PLOT_TRANSPARENTON/OFF. When OFF and the widgets are plotted, what is behind the widget willbe obscured by the top widget. When ON, anything previously plotted behind thewidget will be visible. The default is ON.

Regions, GEOMETRY_OPTIONS.REGIONS



ON/OFF. When ON, regions can be created and manipulated in geometries. Thedefault is OFF.

Scale Solvent, GEOMETRY.SCALE_SOLVENTON/OFF. When ON, and there is a solvent peak in the data file, the solvent peakwill not be included in the calculation of vertical extent in the data. When OFF, alldata points are included in this calculation. The default is OFF.

Sequence, GEOMETRY_OPTIONS.SEQUENCEON/OFF. When ON, sequence analysis information will be displayed ingeometries. The default is OFF.

Sequence Marker, GEOMETRY_OPTIONS.SEQUENCE_MARKERON/OFF. For nD data sets displayed in contour mode. When ON, lines aredisplayed marking the center of each peak. The default is OFF.

Shadow Dimensions, GEOMETRY_OPTIONS.DECIMALSON/OFF. When ON, shadow dimension(s) of each file in geometries are displayedin the upper left corner of the datazone area. The default is ON.

Statistics, GEOMETRY_OPTIONS.STATISTICSON/OFF. When ON, the baseline, +/- threshold, and noise lines are displayed forthe currently selected data in the geometry. The default is OFF.

Positive Levels, GEOMETRY_OPTIONS.POS_LEVELSON/OFF. When OFF, the positive levels will not be visible in 2D contourgeometries. The default is ON.

Negative Levels On, GEOMETRY_OPTIONS.NEG_LEVELSON/OFF. When OFF, negative levels will not be visible in 2D contour geometries.The default is ON.

❏ Geometry Page:Geometry: Hints, GEOMETRY_HINTS_ON *

ON/OFF. When ON, the geometry selectively displays appropriate features for thecurrent cursor mode. When entering a cursor mode, certain features may be turnedon or off. When the cursor mode changes, the geometry features are updated toreflect the defaults for the new mode. When OFF, the geometry features are notchanged with the cursor mode. The default is ON.

Geometry: Persistent Mode, GEOMETRY.HOLD_FEATUREON/OFF. When ON, features that are normally turned off on geometries when theuser switches cursor modes will stay on. For example, go into Peak mode (peaksturn on); go into Integration mode (integrals turn on, and peaks stay on). If OFF,then peaks would turn off in this example. The default is OFF.


Geometry: Peak Unit, GEOMETRY.PEAK_UNITSpecifies the unit that the peaks will be displayed in for geometries that have peakinformation. Some tools allow the peak units to be changed via the pull-downmenus. The default is to display the same units that are the base units of the data.

Geometry: Rotation, GEOMETRY.ROTATIONROTATE/NOROTATE/AUTO_ROTATE. Specifies the initial type of rotation ofgeometries. NOROTATE indicates that the X axis is always horizontal. ROTATEindicates that the X axis is always vertical. AUTO_ROTATE indicates that the Xaxis will be displayed on the longer side of the geometry widget space. The defaultis "AUTO_ROTATE".

Cursor Mode, DEFAULT_CURSOR_MODE *ANNOTATION/CURSOR/DATA/INTEGRATION/MOLECULE/OFFSET/PEAK/PICK/REFERENCE/REGIONS/PIP/ZOOM. The default cursor mode setwhen Delta starts. The default is "DATA".

Border, GEOMETRY_OPTIONS.BORDERON/OFF. When ON, a light blue border is displayed around each PIP window. Thedefault is ON.

Center, GEOMETRY_OPTIONS.CENTERON/OFF. When ON, all lines of text are centered on a widget. For a list box, longlines of text are wrapped if they are too long to display completely. The default isOFF.

Cursor Tool, GEOMETRY_OPTIONS.SHOW_CURSORSON/OFF. When ON, the cursor tool will be available on geometries. The defaultis ON.

Cursor Tool Open, CURSOR_TOOL_OPENON/OFF. When ON, the cursor tool on the geometry widget will be displayed fullsize. When OFF, the tool will be displayed in its closed state. The default is OFF.

Enable, GEOMETRY_OPTIONS.ENABLEON/OFF. When ON, the geometry accepts user interaction. When OFF, the widgetappears 'grey' and does not accept user interaction. The default is ON.

Freeze Slot, GEOMETRY_OPTIONS.FREEZE_SLOTON/OFF. When ON and the geometry is connected to a spectrometer, the data inslot 1 is left unchanged, and subsequent acquisitions are sent to slot 2. The defaultis OFF.

Geom Windows, GEOMETRY_OPTIONS.GEOM_WINDOWSON/OFF. When ON, a light blue border is displayed around areas for which there



is a PIP window active. The default is ON.

Interactive, GEOMETRY_OPTIONS.INTERACTIVEON/OFF. When ON, the widget will react to keyboard and mouse events. WhenOFF, user interaction is ignored. The default is ON.

Molecule Borders, GEOMETRY_OPTIONS.MOLECULE_BORDERON/OFF. When ON, a square border will be visible around all molecules ingeometries. The default is ON.

Molecule Titles, GEOMETRY_OPTIONS.MOLECULE_NAMEON/OFF. When ON, the molecule name will be visible in the upper-left corner ofthe molecule window as well as any text the user has added. The default is OFF.

Molecule Windows, GEOMETRY_OPTIONS.MOLECULESON/OFF. When ON, molecule windows will be visible. The default is ON.

Atom Numbers, GEOMETRY_OPTIONS.ATOM_NUMBERSON/OFF. When ON, the atom numbers will be displayed for every atom in themolecule(s). The default is OFF.

Atom Select Numbers, GEOMETRY_OPTIONS.ATOM_SEL_NUMBERSON/OFF. When ON, the atoms numbers will be displayed only for the atomswhich are selected. If the Atom Numbers preference is set to ON, then thispreference will have no effect. The default is OFF.

Atom Sequence, GEOMETRY_OPTIONS.ATOM_SEQUENCEON/OFF. When ON, the selected atom numbers will be displayed with thesequence information above the peak for which the atom is connected. The defaultis OFF.

Note: Sequence information must be turned on.

No Auto Contour, GEOMETRY_OPTIONS.NOAUTOCONTOURON/OFF. When ON, files added to a geometry will NOT be auto-contoured. Thedefault is OFF.

No Zooming, GEOMETRY_OPTIONS.NOZOOMON/OFF. When ON, zooming and related functions will not function. The defaultis OFF.

Overlay Offset X, OVERLAY_OFFSET_XThe overlay offset on the X ruler (in percentage). A value of zero will not offset theoverlay at all. Negative numbers will offset the data to the left. Positive data willoffset the data to the right. A percentage in the range of -100 to 100 informs thegeometry to shift the data in slots greater than 1 on the X axis.


Thus each slot is shifted (slot - 1) * offset percent. The default is 0.

Overlay Offset Y, OVERLAY_OFFSET_YThe overlay offset on the Y ruler (in percentage). A value of zero will not offset theoverlay at all. Negative numbers will offset the data down. Positive numbers willoffset the data up. A percentage in the range of -100 to 100 informs the geometryto shift the data in slots greater than 1 on the X axis.Thus each slot is shifted (slot - 1) * offset percent. The default is 0.

Overview, GEOMETRY_OPTIONS.OVERVIEWON/OFF. When ON, zoom functions are disabled. Performing a zoom will create aregion instead. The default is OFF.

Peak Threshold On, PEAK_THESHOLDS_ONON/OFF. When ON, peaks will not be able to be created or selected below thethreshold level. An automatic peak-pick will only generate peaks that meet orexceed the threshold. The default is OFF.

Perspective, GEOMETRY_OPTIONS.PERSPECTIVEON/OFF. When ON, multi-dimensional data sets are displayed with theperspective of 3D space -- data is drawn within a frustum. Otherwise, a cube isused for the data display area. The default is ON.

PIP Font Factor, PIP_FONT_FACTORA number representing the scaled font size of a Picture-In-Picture geometry inrelation to the parent's font size. The default is 0.5.

Plot All Text, GEOMETRY_OPTIONS.COLUMNARON/OFF. Used for plotting labels. When ON, text on labels is truncated to 40characters and formatted into columns. The default is OFF.

Process FID, GEOMETRY_OPTIONS.PROCESS_FIDON/OFF. When ON, and the geometry is connected to a spectrometer that iscurrently collecting data, the data displayed will be processed with a Hammingapodization function and an FFT domain transfer function applied. The default isOFF.

Region Manipulation, GEOMETRY_OPTIONS.NOREGIONSON/OFF. When ON, regions cannot be created or manipulated in 3D geometries,but will still be visible. The default is OFF.

Stereo, GEOMETRY_OPTIONS.STEREOON/OFF. When ON, nD data in the geometry will be drawn in stereo vision to beviewed with special glasses. The default is OFF. This feature is not currentlysupported.



Toggle Slot, GEOMETRY_OPTIONS.TOGGLE_SLOTON/OFF. When ON, and the geometry is connected to a spectrometer that iscollecting data, the data will be displayed alternately in slots 1 and 2. The default isOFF.

Track Position, GEOMETRY_OPTIONS.TRACK_POSITIONON/OFF. Used only for Frame widgets. When ON, all Frame widgets whoseparent is the Screen will record information about it’s current size and position onthe desktop. If the window is closed and reopened, it will automatically appear atthe same position with the same dimensions. The default is OFF.

Transparent X Ruler, GEOMETRY_OPTIONS.TRANSPARENT_XRULERON/OFF. When ON, the X ruler markers and grid lines are not displayed. Thedefault is OFF.

Transparent Y Ruler, GEOMETRY_OPTIONS.TRANSPARENT_YRULERON/OFF. When ON, the Y ruler markers and grid lines are not displayed. Thedefault is OFF.

Transparent Z Ruler, GEOMETRY_OPTIONS.TRANSPARENT_YRULERON/OFF. When ON, the Z ruler markers and grid lines are not displayed. Thedefault is OFF.

X Ruler, GEOMETRY_OPTIONS.X_RULERON/OFF. When ON, the X ruler is displayed.

Y Ruler, GEOMETRY_OPTIONS.Y_RULERON/OFF. When ON, the Z ruler is displayed.

Z Ruler, GEOMETRY_OPTIONS.Z_RULERON/OFF. When ON, the Z ruler is displayed.

Positive Levels, LEVEL_TOOL.COMPUTE_LEVELS.POSA number to indicate the positive levels in the data geometry which are initiallycomputed and displayed for a new data set. If all levels are off, Level Tool defaultsettings will be displayed. For example to have only levels 1, 2, and 4 on, one

would set this value to be 20 + 21 + 23 = 11. The default is 0.

Negative Levels, LEVEL_TOOL.COMPUTE_LEVELS.NEGA number to indicate the negative levels in the data geometry which are initiallycomputed and displayed for a new data set. If all levels are off, Level Tool defaultsettings will be displayed. For example to have only levels 4, 7, and 10 on, one

would set this value to be 23 + 26 + 29 = 584. The default is 0.


❏ Cursor Page:

This page has toggles that allow the user to redefine the alternate cursors for each cursormode. The .delta_configure preference has the form, ALT_CURSOR.XXX, where XXX isthe name of each cursor mode. Changes made to these preferences will only take effectonce Delta is restarted.

❏ Colors Page:

These values indicate default colors for Delta Tools and Delta Data. The colors can beselected from the colors defined by X-windows. A list of the colors available can be foundin the Preference Tool, the Widget Editor, or by typing colorview -browse at thecommand prompt in an xwsh terminal shell window.

foreground, FOREGROUND *Black is the default color for widget foregrounds.

background, BACKGROUND *Grey50 is the default color for widget backgrounds.

highlight, HIGHLIGHT *Grey50 is the default for widget highlights.

selected, SELECTED *Yellow is the default selected color for widgets.

datazone, DATAZONE *Black is the default datazone color for widgets.

PM Unselected Color, PRESENTATION_UNSEL_COLORThe color that is used for presentation templates for all regions that are not theselected region. The default is {130,170,255} which is a light blue.

Data Color: Slot n Real, DATA_COLORS_n.REAL *

Data Color: Slot n Imaginary, DATA_COLORS_n.IMAG *Where n is a letter from A through G. These control the color of the displaydata in different slots in a geometry. A through F represent slots 1 through6, where A is the color of the data in the first slot and every 6th slotthereafter; B is the color in the second slot and every sixth slot thereafter,etc. Color G is a grey scale color used if Delta is in Black & White mode.

Peak Color n, PEAK_COLORS_n *n is a letter from A through P. These are the colors of the sequence markers forpeak pick labels. They can be changed using the spreadsheet tool, where A through



P represent Colors 0-16 on the spreadsheet. The default for each preference is“white”.

Molecule Bond Color n, MOLECULE_BOND_COLOR_nn is a number 1 to 10. These are the colors in which the molecule bonds will bedrawn for molecule window n. The default for each preference is “white”.

❏ System Page

Address Book, ADDRESS_BOOK_FILEIf this file is specified, then this file will be used for the address book in the “SendMail” Percival program.

Allow Author Login, ALLOW_AUTHOR_LOGINON/OFF. When ON, the Master Console won’t come up immediately when Deltastarts, instead, a pop-up box lets you select your logon name from a list. Whenyou exit Delta, the popup box has an additional box that allows you to changeyour name, log off and log on as a different user. The default is OFF.

Auto Directory Submit, AUTO_DIRECTORY_SUBMIT *ON/OFF. When ON, any experiment file that is placed in the spectrometerdirectories under /usr/tmp/ will automatically be submitted to the spectrometer.The default is OFF.

Bell Sound, BELLA filename specifying the sounds (.aiff) file to play when the Bell function iscalled. There is not default for this parameter.

Black and White Icons, ICONS_BWON/OFF. When ON, Delta will display all pushbutton icons in black and white.The default is OFF.

Color Mode, DEPTH_8BIT *DITHER/COLOR_INDEX/EXTENDED_COLOR. The color mode in which Deltawill run. This preference applies only to 8 Bit color systems and is ignored on 24Bit color systems. The default is “DITHER”.

Console Log File, CONSOLE_LOG_FILEIf this preference is clear, then logging console lines is off. However, if it is afilename then all Delta Console output is saved in this file. If the filename doesnot include a path, then the ‘Report Output’ path is assumed.

FID Audio, FID_AUDIOON/OFF. The Vector View tool has the ability to show a FID while the experimentis being collected. When ON, the FID will be played through the system's audiohardware. The default is OFF.


Operator Cache, OPERATOR_CACHE *ON/OFF. When ON, Percival operators are cached when loaded. When OFF, everytime an operator is referenced, it must be loaded from disk. The default is ON.

Single Buffering, BUFFERING *ON/OFF. When this value is not any of the values 1, “single”, or OFF, Delta willrun with Double Buffering Mode turned on. The default is OFF.

Spectrometer Monitor, SPECTROMETER.CONTROL.MONITORON/OFF. When ON, and the Spectrometer Tool is connected to a spectrometer, asampling of the spectrometer's current values is displayed on the bottom of thetool. When OFF, this info is hidden.The default is OFF.

Spectrometer Load/Eject Disable, SPECTROMETER.LOAD_EJECT_DISABLEON/OFF. When ON, and the spectrometer has an auto sample changer connectedto it, the Load and Eject buttons will be disabled on the Sample Tool. The defaultis OFF.

❏ Miscellaneous Page

Acquisition Auto-Place, ACQ_AUTO_PLACEMENTON/OFF. When ON, then when a data file comes back from collection, theappropriate data processing tool will appear automatically on the screen. If OFFthen only a red outline will appear and the user must place the tool. Set to ON ifyou will be collecting many data sets and will be away from the workstation. Thedefault is OFF.

Auto Level Tool, LEVEL_TOOL_ONON/OFF. When ON and the first geometry is appears on the desktop, a Level Toolwill automatically appear. The default is OFF.

Auto Console, MASTER_CONSOLE.CONSOLE *ON/OFF. When ON, the console input box is displayed on the bottom of the DeltaConsole when Delta starts. The default is ON.

Console Coloring, CONSOLE_COLORINGON/OFF. When ON, certain types of output to the Delta Console will be colorcoded. The default is OFF.

Console Color, MASTER_CONSOLE.CONSOLE_COLOR *The color for the Delta Console input box. The default is “yellow”.

Console Cut & Paste, MASTER_CONSOLE.CUT_PASTE_TOOLS *ON/OFF. When ON, the cut and paste tools on the Master Console will be



available. The default is ON.

Console History, MASTER_CONSOLE.MAX_LINES *The number of lines in the console that are kept in memory. The default is 512.

Console Wrap, MASTER_CONSOLE.TEXT_WRAP *ON/OFF. When ON, long messages that are sent to the console screen will wrap tothe next line.

Cosy Peak J Width, COSY_PEAK_J_WIDTHThe J-Coupling width (in Hertz or PPM) used for auto peak picking. Peaks withinthis width are considered a single peak and will not be picked more than once.Setting this preference to 0 will disable this feature. The default is 0[Hz].

Geom Tools: Save State, GEOMETRY_TOOLS.SAVE_STATEON/OFF. When ON, the current opened state of the Level Tool is saved in thepreference file. Also when the level tool is displayed or hidden, the“level_tool_on” preference is updated. The default is OFF.

Geom Tools: Tracking, GEOMETRY_TOOLS.TRACKINGON/OFF. When ON, the Level Tool’s position is stored so that when it is restarted,it will reappear at the same location as when it was closed.

Integral Search Width, INTEGRAL_SEARCH_WIDTHThe minimum distance (in Hertz or PPM) two peaks must be separated in order tohave separate integrals created for them. The default is 25[Hz].

Level Tool: Auto Apply, LEVEL_TOOL.AUTO_APPLYON/OFF. When ON, and “Contour Line Check” is also ON, changes made withthe Level Tool will effect the display of the data immediately. The default is OFF.

Level Tool: Pop, LEVEL_TOOL.AUTO_POPON/OFF. When ON, then when the space bar is pressed with the Level Tool open,the Level Tool will be popped to the front. The default is OFF.

Preserve Position, DELTA_TOOLS.PRESERVE_STATEON/OFF. When ON, the size and locations of most Delta tools will remember theirsize and location on the desktop between Delta sessions. A .tool_name.XY_POSconfiguration entry will be placed in the configuration file to store the tools currentsize and position. This will also cause a these tools to be automatically placed onthe screen when they are opened. The default is OFF.

Save Color & Font, SAVE_COLOR_FONTON/OFF. When ON, any colors and fonts that were changed and saved with theWidget Editor will be remembered each time the tool is opened. Otherwise, anymodified features are ignored. The default is OFF.


Show Deconvolution Results, SHOW_DECONVOLUTION_RESULTSON/OFF. When ON, then when data is deconvolved, the results of thedeconvolution will display in the Delta Console. The default is ON.

Show Peak Count, SHOW_PEAK_COUNTON/OFF. When ON, then when data is automatically peak-picked, the number ofpeaks found will display in the Delta Console. The default is OFF.

Sweep/Offset Adjust, AUTOMATIC_SWEEP_OFFSETON/OFF. When ON, and a change is made in the Experiment Tool to anexperiment’s domain parameter on any axis, the experiment automatically updatesit’s corresponding sweep width and offset. The default is ON.

Date Format String, DATE_FORMATA call to the get_date_format operator will return the date/time formattedaccording to this value. The following special characters (shown below in bold) willbe replaced with the appropriate information. The default is “%M %d, %y”.

%m will be replaced by the 3 letter month abbreviation.%M will be replaced by the full Month name.%n will be replaced by the Month number.%d will be replaced by the day number.%w will be replaced by the 3 letter weekday abbreviation.%W will be replaced by the full weekday name.%y will be replaced by the year number.%t will be replaced by the time. (hh - mm - ss)

❏ Tools Page

The Delta Tools page contains user-configurable tool parameter toggles.Automation Console window, otherwise the user will only be allowed to monitor the

spectrometer. The default is OFF.

Allow Connect, AUTO_CONSOLE.CONNECTWhen TRUE, the user is allowed to connect to a spectrometer in the AutomationConsole window; otherwise a user may only monitor a spectrometer.

Connect Tool Init, CONNECT_TOOL.AUTO_INITIALIZEON/OFF. When ON, and the user pushes the Connect button on the Connect Tool,the tool will re-initializes itself to {None, None, None} indicating that the X, Y,and Z axis are ready for a new connection to be set. The default is OFF.

Convert: Auto Extension, CONVERT.AUTOEXTENSIONON/FALE. When ON, automatically fix up the resulting data file extension. Thedefault is ON.



Convert: Quiet, CONVERT.QUIETON/OFF. When ON, progress messages will not be displayed in the status area ofthe Convert Tool. The default is OFF.

Data Slate: Connect X, DATA_SLATE.CONNECT.XON/OFF. When ON, current zoom coordinates will be propagated to othergeometries in the same Data Slate in the X dimension only. The default is OFF.

Data Slate: Connect All, DATA_SLATE.CONNECT.ALLON/OFF. When ON, current zoom coordinates will be propagated to all othergeometries in every dimension.

Note: “Connect X” and “Connect All” cannot both be ON. If this is the case,then “Connect All” has precedence.

Data Slate: Connect Features, DATA_SLATE.CONNECT.FEATURESON/OFF. When ON, and a geometry feature is modified, that change is propagatedto all other geometries in that Data Slate. When OFF, features remain specific toindividual files. The default is ON.

Data Slate: Plot Parameters, DATA_SLATE.PLOT_PARAMSON/OFF. When ON, and a file is printed from Data Slate, the file’s parameters areprinted with the data. The default is OFF.

Data Slate: Plot Process List, DATA_SLATE.PLOT_PROCESS_LISTON/OFF. When ON, and a file is printed from Data Slate, any processing list thatwas stored in the file will be plotted with the data. The default is OFF.

Data Slate: Save Plot Parameters, DATA_SLATE.SAVE_PLOT_PARAMSON/OFF. When ON, the current state of “Data Slate: Plot Parameters” is storedwhen it’s state is changed. The default is OFF.

Data Slate: View Orientation, DATA_SLATE.VIEW_ORIENTATIONHORIZONTAL/VERTICAL/BOX. Sets the default geometry organization forData Slate. The default is “HORIZONTAL”.

Experiment Tool: Hints, EXPERIMENT_TOOL.HINTSON/OFF. When ON, the labels in the Experiment Tool will look like buttons toindicate to the user that clicking on the labels allow the user to modify parametervalues. When OFF, the “button look” is missing, but the user can still click on thelabel to modify the parameter. The default is ON.

File Manager: Delete Whole Dir, FILE_MANAGER.DEL_WHOLE_DIRON/OFF. When ON, and you delete a directory, the File Manager will recursivelydelete all files and other directories in the current directory. When OFF, you will


only be able to delete a directory when it is empty. The default is OFF.

File Manager: Delete Dir Update, FILE_MANAGER.SAVE_DEL_WHOLE_DIRON/OFF. When ON, the current state of the “File Manager: Delete Whole Dir”preference is preserved between Delta sessions. The default is ON.

File Manager: Purge Proc. Query FILE_MANAGER.PURGE_QUERYWhen ON, it pops up a dialog box when the “purge processed” button is pressed inthe file manager. The dialog box prompts the user to press one of the followingbuttons; purge selected file only, purge all files in current directory, purge all filesin current directory and in all sub-directories. The default is OFF.

File Manager: Require Acknowledge, FILE_MANAGER.REQUIRE_ACKON/OFF. When ON, and a potentially hazardous operation isrequested, the FileManager will display an “Are you sure?” message. The default is ON.

File Manager: Require Ack Update, FILE_MANAGER.SAVE_REQUIRE_ACKON/OFF. When ON, the current state of the “File Manager: RequireAcknowledge” preference is preserved between Delta sessions. The default is ON.

File Manager: Show Errors, FILE_MANAGER.COMPILE_ERRORON/OFF. When ON, and compilation from the File Manager results in errors and/or warnings, then a box is displayed with the compilation results. When OFF, theuser is only informed of compilation status by an acknowledge box. The default isON.

File Manager; Show Errors Update, FILE_MANAGER.SAVE_COMPILE_ERRORWhen ON, the current state of the Show Errors preference is saved between Deltasessions.

File Manager: Show Hidden Files, FILE_MANAGER.SHOW_HIDDENON/OFF. When ON, hidden files (those whose filename begins with a “.” inUNIX) are displayed in the directory list box. When OFF, all hidden files anddirectories are not included in the file list. The default is OFF.File Manager: ShowErrors Update, FILE_MANAGER.SAVE_COMPILE_ERRORON/OFF. When ON, the current state of the “File Manager: Show Errors”preference is preserved between Delta sessions. The default is ON.

File Manager: Version Keep, FILE_MANAGER.KEEPSpecifies the number of files to keep when the “Delete All” button is pressed in theFile Manager. Version 1 is always kept and counts toward the number to keep.The default is 2.

PM: Center Y-Scale, PRESENTATION.CENTER_Y_SCALEON/OFF. When ON, the geometry plotted with the Presentation Manager will becentered around 0 and then the data will be Y-scaled to the top of the geometry.



When OFF, the data will be maximized to the extents of the geometry and then Y-scaled. The default is ON.

PM: Font Size, PRESENTATION.FONT_SIZEThe font size to use for plotting data from the Presentation Manager. The defaultis 10.6.

PM: Plot Process List, PRESENTATION.PLOT_PROCESS_LISTON/OFF. When ON, and a box in a Presentation Manager template is set up toprint the acquisition parameters of a file, then the processing list for that data filewill also be printed. When OFF, only the acquisition parameters will be printed.The default is OFF.

Preferences: Start Page, PREFERENCES.START_PAGEThe name or number of the Preferences page that will be displayed when thePreferences Tool is started (e.g., personal).

Sample Tool: Gradient Shim Allowed,SAMPLE_TOOL.GRADIENT_SHIM_ALLOWED

ON/OFF. When ON, the Gradient Shimming buttons will be functional from theSample Tool. The default is OFF.

Sample Tool: Verify, SAMPLE_TOOL.VERIFYON/OFF. When ON, if the user attempts to change the system shims, a pop-up boxis displayed to make sure the user really intends to do this. The default is ON.

Spectrometer Tool: Double-Click, SPEC_TOOL.DOUBLE_CLICK_ACTIONCONNECT/MONITOR. When the user double-clicks on a spectrometer link in theSpectrometer Tool, you will automatically link to the spectrometer in Connect orMonitor mode respectively. The default is “CONNECT”.

Vector View: Auto Off, VECTOR_VIEW.AUTO_OFFON/OFF. When ON, the Vector View tool automatically shuts off the data displayafter 4 minutes. When OFF, the data display is shut off after 30 minutes. Thedefault is ON.

Vector View: Processing, VECTOR_VIEW.PROCESSINGA set of possible processing options to perform prior to display in the Vector Viewtool. The possible strings that may be included in this set are: “DC_BALANCE”,“WINDOW”, “FFT”, “PHASE”, “DC_CORRECT”, “ABS”, and “AUTOPHASE”.


❏ Processors Page

Data Processors:These parameters are used for the Data Processors only:

Process 1D: Auto Apply, PROCESS_ONED.AUTO_APPLYON/OFF. When ON, the “Auto Apply” button will be on (depressed) when 1DProcessor starts. This will cause changes to the processing list to be carried outimmediately. The default is OFF.

Process 1D: Show FID, PROCESS_ONED.FIDON/OFF. When ON, the “original” data window is displayed above the“processed” data window in 1D Processor. The default is ON.

Process 1D: Show Macros, PROCESS_ONED.MACRO_BUTTONSON/OFF. When ON, the row of processing macro buttons is displayed below thetool bar in 1D Processor. The default is ON.

Process 1D: Macro Definition, PROCESS_ONED.MACRO_DEFThe set of operations to perform for each of the 1D Processor macro buttons. Donot attempt to edit this preference directly. Use the editor provided by Process 1D.

Process 1D: Macro Order, PROCESS_ONED.MACRO_PAD_ORDERIndicates the order in which the macro buttons appear in 1D Processor.

Process 1D: View Precision, PROCESS_ONED.VIEW_PRECISIONThe number of decimal places displayed in the view control tool of 1D Processor.The default is 2.

Process 1D: Phase Step P0 PROCESS_ONED.PHASE_STEP.P1Default is 1. Number which indicates the step size of the phase box in the 1Dprocessor.

Process 1D: Phase Step P1 PROCESS_ONED.PHASE_STEP.P0Default is 0.25. Number which indicates the step size of the phase box in the 1Dprocessor.

Process 1D: Plot Parameters, PROCESS_ONED.PLOT_PARAMSON/OFF. When ON, then when data is printed from 1D Processor, the data'sacquisition parameters are printed with the data. The default is OFF.

Process 1D: Plot Process List, PROCESS_ONED.PLOT_PROCESS_LISTON/OFF. When ON, then when data is printed from 1D Processor, the processinglist (if available) is printed with the data. The default is OFF.

Process 1D: Save Auto Apply, PROCESS_ONED.SAVE_AUTO_APPLY



ON/OFF. When ON, then the state of the “Auto Apply” button is preservedbetween 1D Processor sessions. The default is OFF.

Process 1D: Save FID, PROCESS_ONED.SAVE_FIDON/OFF. When ON, then the visibility state of the “original” data window will bepreserved between 1D Processor sessions. The default is OFF.

Process 1D: Save Macro Def., PROCESS_ONED.SAVE_MACDEFON/OFF. When ON, then the macro definitions are saved when they are modifiedso the new definitions will be available in future 1D Processor sessions. Thedefault is OFF.

Process 1D: Save Macros, PROCESS_ONED.SAVE_MACROON/OFF. When ON, then the visibility state of the macro pad will be preservedbetween 1D Processor sessions. The default is OFF.

Process 1D: Save Plot Param, PROCESS_ONED.SAVE_PARAMON/OFF. When ON, then the state of whether or not to print data parameters(indicated by the “Process 1D: Plot Parameters” preference) is preserved between1D Processor sessions. The default is OFF.

Process 1D: Save Simple Mode, PROCESS_ONED.SAVE_SIMPLEON/OFF. When ON, then the “Process 1D: Simple Mode” state is saved each timethat it is changed so that the state is preserved between 1D Processor sessions. Thedefault is OFF.

Process 1D: Save Timing, PROCESS_ONED.SAVE_TIMINGON/OFF. When ON, then the “Process 1D: Show Timing” state is saved each timethat it is changed so that the state is preserved between 1D Processor sessions. Thedefault is OFF.

Process 1D: Save Tools, PROCESS_ONED.SAVE_TOOLSON/OFF. When ON, then the visibility state of the processing tools is preservedbetween 1D Processor sessions. The default is OFF.

Process 1D: Simple Mode, PROCESS_ONED.SIMPLE_MODEON/OFF. When ON, then 1D Processor will start in “Simple Mode”. Otherwise,the processing list features are enabled to provide flexible processing control. Thedefault is OFF.

Process 1D: Show Timing, PROCESS_ONED.TIMINGON/OFF. When ON, the total processing time is displayed on the Delta Consoleeach time the file is processed in 1D Processor. The default is OFF.

Process 1D: Show Tools, PROCESS_ONED.TOOLSON/OFF. When ON, the processing tools in 1D Processor (macro buttons,processing list, and phasing control) will be visible and available to use. The


default is ON.

Process nD: Plot Parameters, PROCESS_ND.PLOT_PARAMSON/OFF. When ON, then the acquisition parameters will be printed with the datawhen printing from nD Processor. The default is OFF.

Process nD: Plot Process List, PROCESS_ND.PLOT_PROCESS_LISTON/OFF. When ON, then the processing list will be printed with the data whenprinting from nD Processor. The default is OFF.

❏ Automation PageAdvanced Automation, AUTOMATION.ADVANCED

ON/OFF. When ON, the Automation Tool comes up with Advanced Mode set onallowing the user to modify some of the experiment parameters before theautomation is submitted. The default is OFF.

Advanced Automation Lock, AUTOMATION.ADVANCED.LOCKON/OFF. When ON, and Advanced Automation is set to OFF, the user will not beallowed to enter Advanced Mode. The default is OFF.

Advanced Automation Sample, AUTOMATION.ADVANCED.SAMPLEON/OFF. When ON, the filename and sample ID will be considered separate andthe user will be able to specify each individually. Otherwise, the filename box willset both the filename and the Sample ID. The default is OFF.

Allow Export Email, AUTOMATION.ALLOW_EXPORT_EMAILWhen ON, a second email address box is shown on the automation window toallow you to specify email address(es) to which to send the collected data sets.When this box is not displayed, it is not possible the send the data via email. Itdefaults to OFF.

Allow Initialize, AUTOMATION.ALLOW_INITIALIZEON/OFF. When ON, and the Automation Tool is in Advanced Mode, the user willbe able to add and modify job parameters. The default is ON.

Append Date, AUTOMATION.DATE_FILENAMEON/OFF. When ON, data files returned from automation will have the date(specified by the “Date Format String” preference) appended to the resultingfilename. The default is OFF.

Confirmation, AUTOMATION_CONFIRMATIONON/OFF. When ON, a dialog box will appear when a method is submitted fromthe Automation Tool requesting confirmation of some parameters. The dialog boxwill time-out in 15 seconds if a response is not given and continue to run thesubmitted method. The default is ON.



Email File, AUTOMATION_EMAIL_FILEIf this preference is specified with a complete path, the indicated file will be mailedto inform users that an automation job is completed. If this is not specified, then adefault message will be sent. There is no default for this parameter.

EMail Hold, AUTOMATION_EMAIL_HOLDON/OFF. When ON, the e-mail line will not be cleared when the Filename or theSlot lines in the Automation Tool are changed. The default is OFF.

Email Limitation, AUTOMATION.EMAIL_LIMITATIONON/OFF. When ON, the user submitting automation templates to run will only beable to select E-mail notification to predefined people. When OFF, the user mayenter any E-mail address. Defaults to OFF.

Gradient Shim, AUTOMATION.GRADIENT_SHIMON/OFF. If ON, then when a method is submitted to the spectrometer, gradientshimming will be executed before the first experiment and also before subsequentexperiments if the lock state is found to be off or the slot has been changed. Thedefault is OFF.

Gradient Shim Allowed, AUTOMATION.GRADIENT_SHIM_ALLOWEDON/OFF. When ON, then Gradient Shimming will available in the Automationmenu. See “Automation: Gradient Shim”. The default is OFF.

Hours, AUTOMATION.HOURSON/OFF. When ON, the automation.hours.machine_ident file will be checkedwhen an Automation method is submitted to the queue. If the expected runtime ofthe entire Method is longer than the allowed time, then the method will be delayed.The default is OFF.

Set Init_Group on Failure, AUTOMATION.INIT_GROUP_ON_FAILURE,When gradient shimming cannot run from Automation, the INIT_GROUPexperiment parameter will be set to this value. If gradient shimming succeeds, thenthe INIT_GROUP parameter will not be modified.

Show Times, AUTOMATION.SHOW_TIMEWhen ON, a dialogue box will appear when a method is submitted fromAutomation showing the estimated time to complete the method. The dialog boxwill automatically choose ‘Continue’ in 30 seconds if the user does not select abutton first.

Supervisor Alert, SUPERVISOR_ALERTThis is the E-mail address of the person who will receive E-mail when a group ofexperiments in Automation does not complete successfully.There is no default forthis parameter.


Supervisor Email Always, SUPERVISOR_EMAIL_ALWAYSWhen ON, E-mail will be sent to the supervisor (specified by ‘Supervisor Alert’)showing the list of experiments that were run when the Method is complete.

Temperature Lock, AUTOMATION.TEMPERATURE.LOCKON/OFF. When ON, the user will not be allowed to modify the temperature valuesset in the automation template. The default is OFF.

Tubeless NMR, AUTOMATION.TUBELESSON/OFF. When ON, the Automation Tool will be enhanced to support liquid(tubeless) NMR. The default is OFF.

PARAMETER CONTROL FILES

delta_parameters.master_listThis file contains a list of common acquisition parameters. This file resides in theuser’s “template” directory. The “template” directory is specified in the.delta_configure file.

delta_parameters.defaultdelta_parameters.1Ddelta_parameters.2Ddelta_parameters.3D

These files contain acquisition parameters, tailored for general, 1, 2, and 3dimensional files, that you would like to appear on plots where the acquisitionparameters are requested to be displayed. They are created from thedelta_parameters.master_list file using the Delta Parameter Editor.If the file(s) are not present then a short list of equation parameters is displayed onthe plot. These files reside in the user's “template” directory. The “template”directory is specified in the .delta_configure file.



USER MENU DEFINITION FILE

.delta_userThis file is used to create a custom menu of commands for the Delta Console andthe Automation Console. This additional menu is titled “User”.The basic layout of the file .delta_user is:

menu-choice | command

where each of the above statements is on a single line.

menu-choice is either a single title designating a menu choice in the “User” menu,or a series of sub-menu titles, separated by > signs, to create a menu choice in asub-menu of the “User” menu.

command is a Percival code element which executes a new program or an opera-tor.

For example:a) to add “File Manager” to the “User” menu, use the following line:

File Manager | new “file_manager”

b) to create an entry “Tic-Tac-Toe” in a “Games” sub-menu in the “User”menu the following line could be used:

Games>Tic-Tac-Toe | spawn eval “tic_tac_toe”

In the above examples, the command new is used to execute a Percival program,and spawn eval is used to execute a Percival operator.

Note: These entries are case sensitive, so type them as you want them to appearin the menu.


ECLIPSE SPECTROMETER FILES AND DIRECTORIES

This section is only applicable to Eclipse and Delta-Upgrade systems that can control aspectrometer.

Root DirectoryThis is the superuser account for the Eclipse system, and normally the only activeaccount on the acquisition system. The initial login directory for this account is the/ directory.

/eclipse/ Configuration Files

❏ gamma.defThis file contains the gyromagnetic ratios for a large number of nuclei.

❏ machine.configThis file is the primary configuration file for the Eclipse+ NMRspectrometer.

Sample machine.config file for an Eclipse+ 300 NMR spectrometer:

------ Machine specific configuration information---- Possible Instrument Types : ECLIPSE+, ECLIPSE, GSX, or PHANTOMINST_TYPE = ECLIPSE+

-- Spectrometer ConfigurationFIELD = 7.0586013 teslaPULSER_TICK = 100.0--ADC = 16/200kHz/60ADC = 16/1MHz/20

-- Oscillator Configuration Table. Channels : obs1 obs2 irr1 irr2 tri qua-- ( Specify Fixed-Oscillator Nuclei as 1H 3H 13C 15N 19F 31P etc. )obs1 = 1H 13C -- HPRCobs2 = NONEirr1 = 1H 13C -- HPRCirr2 = NONEtri = NONEqua = NONE

-- Fixed-Oscillator FrequenciesOSC_1H = 300.40 MHzOSC_3H = 320.40 MHzOSC_13C = 75.45 MHzOSC_15N = 30.35 MHzOSC_19F = 282.65 MHzOSC_31P = 121.50 MHz

-- Field Gradient Controller Type ( NONE, SINGLE_SHAPE, MULTI_SHAPE )GRADIENT = NONE

Eclipse Spectrometer Files and Directories


-- Field Gradient Axis Controllability SettingsFG_CONTROLLABLE_X_AXIS = FALSEFG_CONTROLLABLE_Y_AXIS = FALSEFG_CONTROLLABLE_Z_AXIS = FALSE

-- RF Shaper present/not present for OBS/IRR and TRI/QUA channelsRF_SHAPER_AVAILABLE_OBS_IRR = FALSERF_SHAPER_AVAILABLE_TRI_QUA = FALSE

-- Lagrange Shim System present/not presentLG_SHIMS = FALSE--SAWTOOTH_SHIFT = 7--SAWTOOTH_TRIM = 1.17

-- Auto-Gain ParametersAUTOGAIN_UPPER = 85.0AUTOGAIN_LOWER = 60.0

-- Digital Filter ParametersFILTER_LIMIT = 8MAX_FILTER_POINTS = 65536

-- Number of slots in changer or zero if no changer is presentOPERATION_PROTECT = TRUECHANGER = 0CHANGER_VERSION = 1CHANGER_TIMEOUT = 45SPIN_SLOP = 3.0

-- Source of gas for sample spin operation ( AIR, N2 )SPIN_GAS_SOURCE = AIR

-- low and high temp range of VT unit or 0 0 if no unit is presentVTEMP = -150 180--TEMP_SLOP = 3.0-- Maximum duration in seconds of VT TEMP_HOLD state while sample ejected.TEMP_HOLD_TIMEOUT = 30

-- Low cryogen alarm levels in percentLOW_N2 = 10.0LOW_HE = 25.0

-- Retry and expire times for the file upload managerUPLOAD_RETRY = 15.0 -- minutesUPLOAD_EXPIRE = 10080.0 -- minutes, default 7 days

-- Queue Management ParametersALLOW_OWNED = TRUEALLOW_MONITOR = FALSEIDLE_LOCK = FALSE

-- Queue Delay information in secondsSAMPLE_DELAY = 600.0PROBE_DELAY = 30.0HOLD_DELAY = 600.0

-- Log file turn over control.-- List days of week, separated with spaces, to turn over log-- SUN MON TUE WED THR FRI SAT


MACHINE_LOG = TUE FRIQUEUE_LOG = FRI

--Sound filesREADY_SOUND = /eclipse/ready.aifcSAMPLE_SOUND = /eclipse/sample.aifcPROBE_SOUND = /eclipse/probe.aifcCOLLECTED_SOUND = /eclipse/collected.aifcNOT_COLLECTED_SOUND = /eclipse/not_collected.aifc

-- CPF/GSX/GX Specific parameters--GSX_AUTOLOCK_TRANS = 255--SAWTOOTH_SHIFT = 9--SAWTOOTH_TRIM = 1.22

-- AQP3 ADC pipeline depthADC_PIPELINE_DEPTH = 1

-- Strictly Enforce Solvent Temperature Limits during experiments.STRICT_SOLVENT_TEMP_LIMITS = FALSE

-- Shim knob box presentSHIM_KNOB_BOX = FALSE

-- Shim knob box Load/Eject, Spin, Lock buttons disabled on EX instrumentsSHIM_KNOB_BOX_LOCKOUT = TRUE

-- Operate B-bus devices in CONNECT mode.CONNECT_DEVICES = TRUE

❏ Standard machine.config file entries

Below is a complete list of the spectrometer configuration parameters. Many of these areused to enable specific accessories or special features available only to spectrometersequipped with certain hardware systems. Use any configuration parameters not appearingin the distributed machine.config file with caution.

ADCDefines the resolution and speed of the installed Analog-to-Digital Converters. Theentries are in pairs. The first number is the digital range of the ADC in bits. Thesecond number is the maximum speed of the ADC in Hertz. If more than one ADCis in the acquisition system they can be appended to this entry separated by aspace.

ADC_PIPELINE_DEPTHSpecifies which type of ADC board is being used in the Acquisition System. ForADC boards with two BNC Twin-Ax connectors: ADC_PIPELINE_DEPTH = 1.For ADC board with two JST 3-pin connectors: ADC_PIPELINE_DEPTH = 3.The default is 3.

ALLOW_MONITORThis field indicates whether more than one Delta workstation can connect to the



instrument and get back real-time views of the data as it is acquired. The default isFALSE.

ALLOW_OWNEDWhen this flag is TRUE, it allows the Eclipse spectrometer to operate in Connector Console (single user) Mode. It is then said that the user “owns” thespectrometer. When this flag is FALSE, the user may only enter Monitor Mode onthe spectrometer, and only users with console privilege can “own” thespectrometer. “Owning” the spectrometer allows the user to run “interactiveexperiments” such as sawtooth. If the user does not “own” the spectrometer,experiments may only be submitted to the experiment queue. The default isTRUE.

AQP3_VERSIONSpecifies the AQP3 board version: (0 or 1). The default is 0.

AUTOGAIN_LOWERAUTOGAIN_UPPER

These entries define the lower and upper limits, in percent, for the Free InductionDecay signal intensity when using the automatic gain-setting feature. ForAUTOGAIN_LOWER, the default is 60.0. For AUTOGAIN_UPPER, the defaultis 85.0.

BBUS_INTERFACE_BOARDSpecifies whether or not the instrument is equipped with a B-Bus Interface Board.The default is FALSE.

CHANGERDefines the number of samples that the installed Auto-Sample Changer can hold atone time. Systems without an Auto-Sample Changer have a value of 0. CurrentlyJEOL supplies 3, 8, 16, and 64 sample changers. The default is 0.

CHANGER_MAX_CHANGE_TIMESpecifies the maximum time, in seconds, allowed for completion of an Auto-Sample Changer load or store operation before a time-out condition can berecognized and acted upon. The default is 45 seconds.

CHANGER_TIMEOUTSpecifies the maximum time, in seconds, allowed for completion of an Auto-Sample Changer load operation before an experiment that requires the specifiedsample slot is moved down in the experiment queue to be attempted later. Thedefault is 300 seconds.

CHANGER_VERSIONDefines the Auto Sample Changer software ROM version:0 = pre-Eclipse+ and 1 = Eclipse+ The default is 0.


COLLECTED_SOUNDThe location of the sound file used to inform the user that an experiment hascompleted successfully.

CONNECT_DEVICESSpecifies whether instrument B-Bus hardware devices are to be operated inconnected or disconnected mode. This setting affects the alarm presentationbehavior of B-Bus devices. The default is FALSE.

FG_CONTROLLABLE_X_AXISFG_CONTROLLABLE_Y_AXISFG_CONTROLLABLE_Z_AXIS

Specifies whether field gradient control is available on the X, Y and Z axes,respectively. Default to FALSE.

FIELDDefines the magnetic field strength, in Tesla, for the Eclipse spectrometer. Thisvalue is used with the gamma.def file to calculate the actual observationfrequencies of the desired nucleus.

FILTER_LIMITSpecifies the maximum number of times that the data can be over-sampled whendigital filtering is turned on. The default is 8.

GRADIENTSpecifies field gradient controller type: (NONE, SINGLE_SHAPE,MULTI_SHAPE). The default is NONE.

GSX_AUTOLOCK_TRANSSpecifies the threshold at which the autolock value in the solvent.def file ischanged to 0 or 1 for the GSX/GX/CPF lock modules. The default is 0.

GSX_COMPATDefines whether this instrument is compatible with instrument control as definedfor a GSX spectrometer. The default is FALSE.

HOLD_DELAYDefines how long the Eclipse acquisition system will wait for the host to completedata processing and submit a new experiment with parameters determined from themost recent experiment. The default is 600.0.

IDLE_LOCKControls whether the machine.idle_lock file is executed when there are noexperiments in the queue and no one owns the spectrometer. The default is FALSE.



IDLE_LOCK_DELAYSpecifies the delay, in seconds, after the conditions for execution of themachine.idle_lock file exist, to wait before entering the idle_lock state.Default to 120.0.

INST_TYPEDefines the machine type. Supported machine types are Eclipse+, Eclipse, GSX,and Phantom. The GSX instrument type is used for JEOL GX, GSX, and CPFNMR spectrometers. The Phantom instrument type is used to demonstrateexperiment control when a spectrometer is not available. The default is ECLIPSE.

LG_SHIMSSpecifies whether there is a Lagrange Shim system connected to the spectrometer.The default is FALSE.

LOCK_TIMEOUTThe length of time in seconds that the sample queue will wait for the lock toindicate “lock on”. The default is 300.0.

LOW_HEDefines the level, in percent, at which the helium warning light on the front of theEclipse acquisition system will come on. The default is 10.0.

LOW_N2Defines the level, in percent, at which the nitrogen warning light on the front of theEclipse acquisition system will come on. The default is 10.0.

MACHINE_LOGThis entry defines the days of the week that the machine.log file is turned overto the machine.old file for Sunday through Saturday. The default is (FALSE,FALSE, FALSE, FALSE, FALSE, FALSE, TRUE)

MAGNET_DRIFT_RATE_HZ_PER_HRSpecifies the magnetic field drift rate in Hz per hour. A value of 0.0 causes theautomatic magnetic-field drift-correction function to be inactive. When a loadsystem shim call is issued, the software calculates the time difference betweencurrent time and the last time the system shims were save and corrects the Z0 shimautomatically. This action is not carried out if the value = 0.0.Note: It is important that the spectrometer be still shimmed on a regular basis andthe system shims saved to disk.The default value is 0.0.

MAX_FG_PULSESpecifies the maximum duration, in seconds, that the multi-shape field gradientamplifier can safely drive its outputs at 100% power. The default is 100.0E-3. (1/10second).


MAX_FILTER_POINTSSpecifies the maximum number of points that can be digitally filtered.FILTER_FACTOR * X_POINTS cannot be larger than MAX_FILTER_POINTS.The default is 64 * 1024.

MAX_POINTSDefines the maximum number of data points collected in a single experiment. Foran AQP3, the default is 1024 * 1024. For other units, the default is 512 * 1024.

MAX_PULSE_SEQUENCE_BYTESDefines the maximum size, in bytes, of the compiled pulse sequence for downloadto the pulsar. The default is 8192.

MAX_SCANSDefines the maximum number of experiment scans allowable in an experiment.The default is 2**15 - 1.

MINIMUM_LOCK_STRENGTHDefines the minimum value of lock-signal strength sufficient to insure that the lockoscillator is functioning. The default is 50.0.

NOT_COLLECTED_SOUNDThe location of the sound file used to inform the user that the experiment was notcollected successfully.

OBS1, OBS2, IRR1, IRR2, TRI, QUAThese entries define what type of oscillator is available to each RF channel. Thevalues for each RF channel are specified as the atomic number followed by theperiodic table element symbol. To specify a High Precision Offset for any channel,remove the “--” before the “HPRC” designator. This will cause the channel to betreated like a High Precision Offset by the Control software.

OPERATION_PROTECTControls the multitasking abilities of an Eclipse NMR spectrometer. When set toTRUE, only one operation at a time is allowed on the spectrometer. The default isTRUE.

OSC_1H, OSC_3H, OSC_13C, OSC_15N, OSC_19F, OSC_31PThese entries define the fixed oscillator frequencies for those nuclei for whichfixed oscillators are manufactured. The values shown below are typical for a 300MHz spectrometer.

OSC_1H = 300.40 MHzOSC_3H = 320.40 MHzOSC_13C = 75.45 MHzOSC_15N = 30.35 MHz



OSC_19F = 282.65 MHzOSC_31P = 121.50 MHz

PRESERVE_DIALS_FILESpecifies whether the xxxx.dials file for an autotune probe should be deletedupon instrument power-up. The default is FALSE.

PROBE_DELAYDefines how long, in seconds, the Eclipse acquisition system will wait for theprobe to be changed before shifting the waiting experiment down in the queue. Aspecific probe must be requested in the experiment for this feature to be active. Thedefault is 30.0.

PROBE_SOUNDThe location of the sound file used to prompt the user to check the probe tuning.

PULSER_TICKDefines the minimum pulser tick in nanoseconds for the NMR spectrometer. Thedefault is 100.0.

QUEUE_LOGDefines the days of the week that the queue.log file is turned over to thequeue.old file for Sunday through Saturday. The default is (FALSE, FALSE,FALSE, FALSE, FALSE, FALSE, TRUE).

READY_SOUNDThe location of the sound file used to inform the user that the spectrometer hasfinished its boot-up procedure.

RF_SHAPER_AVAILABLE_OBS_IRRRF_SHAPER_AVAILABLE_TRI_QUA

Specify whether an RF Shaper accessory is installed for use with the OBS and IRRchannels, and for the TRI and QUA channels, respectively. Defaults are FALSE.

SAMPLE_DELAYDefines how long, in seconds, the Eclipse acquisition system will wait for thesample to be changed before shifting the waiting experiment down in the queue.The default is 600.0.

SAMPLE_SOUNDThe location of the sound file used to prompt the user to select a non-null sample idfor a submitted experiment.

SAWTOOTH_SHIFTThis field sets the reference point for sawtooth mode in the GX/GSX/CPF lockmodules. The default is 6.


SAWTOOTH_TRIMThis field adjusts the end points of the sawtooth range for the GX/GSX/CPF lockmodules. The default is 1.0.

SHIM_KNOB BOXSpecifies whether there is a Shim Knob Box connected to the spectrometer. Thedefault is FALSE.

SOUND_DURATIONThe length of time in seconds that a sound event is repeated. The default is 45.0.

SPIN_GAS_SOURCESource of the pressurized gas for sample spin operation: (AIR or N2). The defaultis AIR.

SPIN_SLOPDefines the slop, in Hertz, within which sample-spin setpoints are considered metto allow experiments to proceed. The default is 3.0.

SPIN_TIMEOUTThe length of time, in seconds, that the sample queue will wait for the sample spinspeed to converge to within SPIN_SLOP of the desired spin speed setpoint beforea fault may be recognized. The default is 120.0.

STRICT_SOLVENT_TEMP_LIMITSAllows strict enforcement of solvent freezing and melting temperature limits,causing pop-up dialog boxes to display warning messages. Forces temperaturelimits violations to kill experiments when set to TRUE. The default is FALSE.

SUPPRESS_FW_WARNINGSSpecifies the version of instrument control software, in the formatMAJOR.MINOR, which is expected to be run on the instrument. If a differentversion is run, checks if instrument firmware versions will be performed each timean experiment is started, and if dialog boxes that warn of older-than-latest versionswill be displayed. The default is 0.0.

SYNC0_BUS_LINESYNC1_BUS_LINESYNC2_BUS_LINESYNC3_BUS_LINE

Specify the instrument sync-bus masks for triggering the AQP3 unit’s sync0through sync3 lines. Defaults are 31.

TEMP_HOLD_AVAILABLESpecifies whether the TEMP_HOLD variable temperature control feature is



available. The default is TRUE.

TEMP_HOLD_TIMEOUTSpecifies the maximum duration, in seconds, that the TEMP_HOLD state can existwhile the sample is ejected. The default is 120 seconds.

TEMP_SLOPDefines the slop, in degrees Celsius, within which temperature setpoints areconsidered met to allow experiments to proceed. The default is 2.0.

TEMP_TIMEOUTDefines the maximum time, in seconds, to wait for a temperature setpoint toconverge to within TEMP_SLOP of the requested setpoint before posting awarning message. This time-out is in effect for experiments that do NOT use theSETTLE_VT header flag. The default is 600.0.

TRIM_Z0_WHEN_LOCK_ONSpecifies whether the automatic magnetic-field drift-correction function is activeduring the LOCK ON state. For long term experiments, which are being acquiredwith the lock on, this correction can be included.Example:MAGNET_DRIFT_RATE_HZ_PER_HR = 6.4Z0_HZ_PER_TICK = 2.0TRIM_Z0_WHEN_LOCK_ON = TRUE

When TRUE, drift correction can occur while LOCK is ON.When FALSE, drift correction cannot occur while LOCK is ON, but resumes when

LOCK is OFF. The default value is FALSE.

TSC_AVAILABLESpecifies whether a Tubeless Sample Changer is connected to the spectrometer.The default is FALSE.

TSC_TIMEOUTSpecifies the maximum time, in seconds, allowed for completion of a TubelessSample Changer load operation before the experiment is moved down in theexperiment queue. The default is 300 seconds.

UPLOAD_EXPIREDefines the maximum amount of time, in seconds, that the Eclipse spectrometerwill spend trying to upload a file when the user who submitted the experiment isnot connected to the Eclipse spectrometer. The default is 6000.0.

UPLOAD_RETRYDefines how often, in minutes, the Eclipse spectrometer will try to upload a filewhen the user who submitted the experiment is not connected to the Eclipsespectrometer. The default is 10.0.


VTEMPDefines the absolute temperature extremes for operation of the variabletemperature control system. These limits apply until superseded by any morestringent constraints found in a probe file. The default is 0 0. (This represents VTcontrol unavailable).

Z0_HZ_PER_TICKSpecifies the change in Hz that result from a unit change in the value of the Z0shim setting. For 300 and 400 MHz systems a single tick change of Z0 does notcorrespond to a 1[Hz] change. For these systems the relationship needs to beexperimentally determined. We have determined that this value is roughly 2[Hz]per tick.Note: For 500 MHz and higher this value should be set to 1.0.

The default value is 1.0.

❏ machine.lg_shimsThis file describes the names, ranges, increments, and units for the Lagrange shimsystem.

❏ machine.mx_shimsThis file describes the names, ranges, and increments for the matrix shim system.

❏ machine.infoThis file contains the spectrometer information text that is displayed when the infobutton is pressed on the spectrometer connection tool. A connection to aspectrometer is required before this information can be viewed. The '|' is used toindicate a new line in the display.

Sample machine.info file:

Eclipse 270 NMR Spectrometer|H/C Observation|H/C Irradiation|Variable Temperature Range: -150C to 180C

❏ machine.poll_speedsThis file defines the standard polling rates in seconds for the instrument parameterslisted in the file. These are the times between which measurements of theappropriate hardware are taken. Parameters not listed in this file are only polled onreference.

Sample machine.poll_speeds file:



LOCK_STRENGTH = 5LOCK_PHASE = 60LOCK_STATUS = 5SPIN_GET = 5TEMP_GET = 10SAMPLE_STATUS = 5SPIN_STATUS = 5TEMP_STATUS = 5N2_LEVEL = 600HE_LEVEL = 600AUTOSHIM_MODE = 20SHIM_MAX_RECALL = 10

❏ queue.hoursThis file controls the time limits for experiments submitted to the queue. The firstsection defines the length of the ten time slots. The second section defines theusage of the time slots. An experiment submitted will be delayed until thecalculated duration is shorter than the current slot time length. Times which are notspecified are infinite. This feature can be used to limit the length of experimentsduring prime-time hours.

Sample queue.hours file:

-- Time lengths in minutes. Non-specified times are infinite.1 1802 3003 4804 36005 144067890-- Day/hour duration assignments. Non-specified blocks are infinite.-- Note 24 hour time.hrs 012345678901234567890123sunmon 333333311111111111222233tue 333333311111111111222233wed 333333311111111111222233thr 333333311111111111222233fri 333333311111111111444444sat


❏ queue.prioritiesThis file controls the priority of experiments that the user submits. This will allowprojects or users to have experiments moved up or down the queue depending onthe assigned priority. The user name in this file must match the user name in theuser's .delta_configure file. The range of priorities is 0 to 255.

Sample queue.priorities file:

-- Queue priorities set by author name from the delta_configure file-- the default priority for names not in this table is 32Mark = 33Steve = 42

❏ solvent.defThis file defines the lock parameters for many standard solvents. Entries in this fileinclude for each solvent: solvent name, solvent abbreviation, lock offset, locklevel, lock gain, autolock level, melting point, and boiling point. The lock offsetsin this file define a chemical shift reference of 0.0 for a domain offset of 0.0 forprotons. Other nuclei are also defined this way, but solvent effects will cause somedeviation from zero for a standard reference compound. The melting and boilingtemperatures for the solvent are used to warn the user when the VT system is set toa temperature that might freeze or boil the solvent.

Machine action files


MACHINE ACTION FILES

These files are used to set default states of the instrument at different times during thenormal operation of the Eclipse NMR Spectrometer. A complete list of possibleparameters can be found in the Parameter tool located on the Spectrometer Controltool.

❏ machine.connectThis file is run when the user connects to the Eclipse NMR Spectrometer.

❏ machine.defaultsThis file is executed before every experiment or job group of experiments.

Sample machine.defaults file:

-- Default parameter values loaded before experiment and upon connectionRECVR_GAIN = 8.0SPIN_SET = 15.0SPIN_STATE = SPIN ONTEMP_STATE = TEMP OFFTEMP_SET = 26.0LOCK_OSC_STATE = 2H OSC ONSAWTOOTH_RANGE = 4

❏ machine.idle_lockThis file is executed when the machine is idle and no one is connected to it.Normally this file is used to leave a standard sample in the magnet on instrumentsthat have an Auto-Sample Changer.

Sample machine.idle_lock file:CHANGER_SAMPLE = 1SOLVENT = CHLOROFORM-DLOCK_STATE = AUTOLOCK

❏ machine.pre_expThis file is executed before a new job group of experiments is run on a particularsample. This file is run if:

- the automatic flag is TRUE in the experiment header section,- the user owns the Eclipse NMR Spectrometer,- the pre_post flag is TRUE in the experiment header section.

This file is also run if the user does not own the Eclipse NMR Spectrometer andthe pre_post flag is TRUE in the experiment header section.


❏ machine.post_expThis file is executed after a job group of experiments is run on a particular sample.This file is run if:

- the automatic flag is TRUE in the experiment header section.- the user owns the Eclipse NMR Spectrometer.- the pre_post flag is TRUE in the experiment header section.

This file is also run if the user does not own the Eclipse NMR Spectrometer andthe pre_post flag is TRUE in the experiment header section.

/eclipse/probes/

This directory contains files that specify parameters for individual NMR probes. Eachprobe can have up to 4 files: xxxx.probe, xxxx.shims, xxxx.limits,and xxxx.dials. xxxx is the 4 digit probe number that is unique to each type ofJEOL NMR probe.

❏ xxxx.probeThis file describes the default spectroscopic and tuning parameters for a specificNMR probe.

Sample xxxx.probe file:

probe 5mm_Broadband 1412 Tunable Proton 1H Carbon 13C

irr_code = 146 90 = 10.0 10.0 50.0 spin_lock_90 = 100 spin_lock_attn = 29 . . temp_limit_hi = 150 temp_limit_lo = -100 . . . . temp_limit_hi_max = 160.0 temp_limit_hi_min = 20.0 temp_limit_md_max = 50.0 temp_limit_md_min = -40.0 temp_limit_lo_min = -110.0 . . . .



vt_pid_std_nb_h_pb = 1.3 vt_pid_std_nb_h_ti = 29 vt_pid_std_nb_h_td = 5 vt_pid_std_nb_h_cbl = 10.0 vt_pid_std_nb_h_cbh = 0.0 vt_pid_std_nb_h_hc = 2.4 vt_pid_std_nb_h_hl = 70 . .

(Other "vt_pid_" values not shown here for brevity.) domain 1H 90 = 10.4 18 50 probe_tune = 0000 probe_match = 2625 end 1H domain 13C 90 = 8.3 8.2 39 probe_tune = 2770 probe_match = 5145 probe_coarse = NONE end 13C domain 29Si 90 = 10.2 10.2 40 probe_tune = 5040 probe_match = 4860 probe_coarse = A end 29Si domain 31P 90 = 7.6 7.6 38 probe_tune = 4870 probe_match = 5390 probe_coarse = X end 31P domain 15N 90 = 14.7 14.7 60 probe_tune = 3500 probe_match = 2745 probe_coarse = E end 15Nend probe

Note: The values in the program above specify the temperature PIDparameters for this probe when operating in various modes.


The “std.” qualifier specifies STANDARD duration VT control.The “long” qualifier specifies LONG duration VT control.The “nb” qualifier specifies NARROW magnet bore.The “wb” qualifier specifies WIDE magnet bore.The “_h_” qualifier specifies HIGH temperature operating range.The “_m_” qualifier specifies MID temperature operating range.The “_l_” qualifier specifies LOW temperature operating range.The “_0_” qualifier specifies 0-DEGREE-C offset mode.The “_40_” qualifier specifies -40-DEGREE-C offset mode.

Explanation of xxxx.probe file entries:

probe This field is used to describe what types of nuclei and experimentsfor which the probe can be used. These include, but are not limitedto: 5mm_Broadband, 5mm_C/H, 10mm_Broadband, Tunable, C/H,Autotune, HX, Proton, 1H, Carbon, 13C, 19F, and Fluorine.

irr_code This field defines the default irradiation code for the 1H decoupler.The meaning of this code can be found in Chapter 10.

90 This field defines the default 90˚ pulses for nuclei not explicitlydefined in the xxxx.probe file. The first value is the observe 90˚pulse width, the second value is the high power irradiation pulse90˚ width used for polarization transfer experiments, and the thirdvalue is the decoupling 90˚ pulse width used for pulse decouplingsequences.

spin_lock_90 This field is the proton 90˚ pulse width for spin-lock and isotropicmixing experiments.

spin_lock_attn This field is the proton channel attenuator setting for spin-lock andisotropic mixing experiments.

temp_limit_hitemp_limit_lo These fields indicate the temperature limits of the probe. Delta will

not allow these limits to be exceeded.

domain X ...end domain These entries are used to define the scope of parameters used for a

specific nucleus. Entries for a particular domain are used only whenthat nucleus is used in an experiment.

probe_tune Defines the default probe tune values for tuning the nucleusspecified by the current domain.



probe_match Defines the default probe match values for tuning the nucleusspecified by the current domain.

probe_coarse Defines the coarse probe tune value for tuning the nucleus specifiedby the current domain. This can be either a specific probe tuningstick on a broadband probe or the dial position on an autotuneprobe. HF is used to select the proton / fluorine channel for theautotune probe.

Note: Other machine parameters may also be defined for a specific domain.These have the same form as the parameters contained in the machine actionfiles.

❏ xxxx.shimsThis file contains the standard system-wide shim settings for the probe. These canbe updated by connecting to the Eclipse NMR spectrometer as console and usingthe Save System Shims in the pull-down menu. Only users connected as consolemay update this file.

❏ xxxx.shims.0This file contains the system shim file prior to the current one.

❏ xxxx.limitsThis file contains the tuning limits for the dials on an autotune probe. Do notchange the values in this file, the autotune probe will be damaged!

❏ xxxx.dialsThis file contains the current values for the dials on an autotune probe. This file iscreated and updated by the Config Autotune Probe Tool on the SpectrometerControl Tool.

/eclipse/shapes/

This directory contains files that numerically describe functions used in certain typesof NMR experiments requiring RF shaping, or magnetic field gradient control. Eachfile is an ASCII text list of up to 1024 floating-point numbers used by the acquisitionsystem to selectively attenuate an RF signal (as in an experiment requiring RFshaping), or to create a time-varying magnetic field gradient.

There are two types of shape files: fixed and user-definable. The user-definable shapefiles must be created with the names user0.shape through user9.shape. A user-definable shape file can contain from 3 to 1024 floating-point numbers.


When an NMR experiment requiring RF shaping or magnetic field gradient control isrun, the acquisition system splines a smooth curve to fit the data in the.shape file andapplies this function to the shaped pulse in the experiment. The shaped curve willrepresent the smoothest curve possible within the time constraints of the shapedpulse's duration.

eburp1.shape left_half_sinc.shape right_half_sinc.shapeeburp2.shape left_half_sine.shape right_half_sine.shapegauss.shape ramp_down.shape seduce.shapeiburp1.shape ramp_up.shape sinc.shapeiburp2.shape reburp.shape sine.shapeleft_half_gauss.shape right_half_gauss.shape uburp.shapeuser0.shape

/eclipse/ Program Files

❏ aqp_programThis file is the program that is loaded into the acquisition processor to control thedata acquisition rates and sizes.

❏ config_modem.shThis program is run by the installation program to configure and initialize themodem.

❏ control_aqp2, control_aqp3This program controls all the Eclipse NMR spectrometer sub-systems includingthe acquisition processor, the pulser, the slow I/O peripherals, the Disk I/O, and thecommunication with the host Delta workstation.

Help output from the control program:

./control [-hfqmprivn] -h Display this message -f Disable Powerfail experiment recovery -q Disable experiment logging -m Disable machine logging -c Disable machine communications -p Disable Loading pulser -r Disable Power on reset -i Disable idle lock on startup -v Display Version -n Do not start



Switches:-h Displays the list of switches for control and a short description of each switch's

function.-f Disables the powerfail experiment recovery. Prevents any experiments remaining in

the queue when control was terminated from automatically restarting.-q Disables the logging of experiment sample messages to the queue.log file.-m Disables the logging of spectrometer messages to the machine.log file.-c Disables communications with the SCON module, the slow I/O peripherals, and the

pulser.-p Disables the loading of the pulcon.pul program into the pulser.-r Disables the power on reset of the spectrometer modules when control is started.-i Disables the machine.idle_lock action file.-v Displays the version information for the Control program.-n Causes control to load, execute the v switch if present and exit.

❏ eclipseThis file is a Bourne shell script file run at boot time. It will restart Control if itcrashes due to a hardware or software failure.

Sample eclipse script file:

#!/bin/shexec >/dev/null 2>&1cd /eclipseHOME=/export HOMEif /sbin/chkconfig aqp2; then

npri -h 30 /eclipse/control_aqp2 >/dev/null 2>&1while /bin/true; do

npri -h 30 /eclipse/control_aqp2 -p >/dev/null 2>&1done

elsenpri -h 30 /eclipse/control_aqp3 >/dev/null 2>&1while /bin/true; do

npri -h 30 /eclipse/control_aqp3 -p >/dev/null 2>&1done

fi

❏ gxscon.scnThis file is used for Eclipse spectrometer initialization when the spectrometer ispower on.

❏ machine.alarmsThis file contains a listing of the possible alarms generated in the Eclipse


spectrometer due to a hardware failure.

❏ machine.authorizationThis file controls a user's access to machine features, and consists of a user namefollowed by a list of restrictions.

❏ make_copyThis program is used to make a copy of a currently running experimental data fileand upload it to Delta. The make_copy program allows for the monitoring of anexperiment's progress.

❏ pulcon.pulThis file is the pulser control program. It is downloaded to the pulser when thespectrometer is powered on.

❏ /usr/eclipse/This directory contains log files that result from machine operation and data fileswaiting to be uploaded to a Delta workstation for processing and display.

❏ cryogen.logThis file contains a log of the cryogen levels in the instrument.

❏ machine.logThis is the instrument log file. It contains all the messages that are normallyprinted on the Delta Console for this instrument. It also contains additionalinformation about hardware errors that may be occurring in the AcquisitionSystem.

❏ machine.oldThis is the second most recent machine.log file. The machine.log files are restartedon a schedule defined in the machine.config file. New logs start with the first entryafter midnight on the day defined in the machine.config file.

❏ queue.logThis is the current sample log for the instrument. It contains entries for eachsample that was run. This file also lists which user ran the experiment, when theexperiment was run, how long the experiment was scheduled to take, and how longthe experiment actually took.



❏ queue.oldThis is the most recent queue.log file. The queue.log files are restarted on aschedule defined in the machine.config file. The new logs are started with the firstentry after midnight on the day defined in the machine.config file.

/usr/eclipse/testprogs/

These programs and files are used for testing the Eclipse acquisition hardware.

❏ blink.cofThis file is downloaded to the Acquisition Processor with the download program.If the download is successful, the user light on the Acquisition Processor will blinkuntil the program is terminated.

❏ countThis program will determine the number of Acquisition Processors installed in theAcquisition System VME Chassis.

❏ downloadThis program is used to download Acquisition Processor *.cof files and startprogram execution.

❏ hw_debugThis program is a spectrometer hardware-debugging utility for use by field serviceengineers only.

Warning: Only service engineers can use this utility, and JEOL is notresponsible for any damages incurred by using it.

❏ ident_sippThis program is used to test the memory of the AQP-III Data Acquisition Board.

❏ interrupt.cofThis file is downloaded to the Acquisition processor with the interrupt_testprogram.

❏ interrupt_testThis program tests the VME interrupt handshaking between the Acquisitionprocessor and the SGI V35 CPU. Count is the number of times required to run theinterrupt test. Value is the number loaded into the Acquisition Processor to test


specific values for data transfer.

Help output from the interrupt_test program:./interrupt_test count coff_filename [value]

❏ test_lightsThis program will test the indicator lights on the front of the Acquisition Systemchassis.

❏ test_serial_fiberThis program is used to test the Serial Fiber Optic connection board. This testrequires a fiber optic loop-back cable.

/etc/init.d

❏ localThis file is used to automatically start the eclipse script when the system is booted.

#!/sbin/sh#Tag 0x00000f00

case "$1" in `start')rm -rf /lost+found/*/eclipse/eclipse &;;

`stop')killall eclipse control_aqp2 control_aqp3;;

*)echo "usage: $0 {start|stop}";;esac

SAMPLES

DELTA User’s Guide, v 3.2 F-1

APPENDIX F: DESCRIPTION OF THE AUTOMATION

TEMPLATE FILE

An Automation Template file is a ASCII file generated by the Automation Editor(see below) and read by the Automation program. The template file contains instructionsfor a spectrometer to carry out one or more experiments. This description is intended to givethe user an understanding of what the template file contains.

There are two main categories of instructions in a template file. A SAMPLEstatement and a METHOD section. There may be more than one of each, and they may bewritten in any order. In some instances, Methods may depend on Samples that have beendefined with the SAMPLE statement. In these cases, the SAMPLE definition must precedethe METHOD section that depends on it.

In this short overview, items placed in brackets, [ ], will be considered optional itemsfor the syntax and may be omitted. Items separated by a vertical bar indicate that a choicemust be made for one item only.

SAMPLES

Samples are useful for declaring sets of named attributes for which an experimentwill be run on. Declaring more than one Sample and including the titles in the GROUPsection allows repetition of experiments without having to write an Experiment declarationfor each Sample for which you'd like to collect data.

Here is an example of a SAMPLE statement:

SAMPLE sample_name ISSAMPLE_ID"001_56"[COMMENT"This is a test sample"]SLOT 2SOLVENT"CHLOROFORM-D";

The words which are capitalized and not in quotes are keywords. Sample_name isthe title given to this group of sample attributes, namely the sample_id, comment, slot torun on, and solvent to use. The comment field may be omitted in which case it will be setto "". See the EXPERIMENT definition for a description of each of the four attributes.

F-2 DELTA User’s Guide, v 3.2

METHODS

The Method section is defined as follows:

METHOD method_name IS [ADVANCED]

[PRINTER "my_printer"][HELP "This is the help text"]

GROUP.....END GROUP;.[ <more groups> ]

END METHOD;

The keyword ADVANCED on the first line of the METHOD section is optional. If it isomitted, then the experiments contained within this Method will run immediately whensubmitted. If the Method is declared to be advanced (by including this keyword after theIS), then when the Method is run, a pop-up box will appear allowing the user to modifymany of the values of the experiment parameters. This will not be discussed further here.

The second line beginning with the keyword PRINTER is also optional. The printer entrydefines the printer for which the experiments in this method will be plotted. Entries mustexist in the .delta_configure file for this to work properly. If any or all of the entriescannot be found in the.delta_configure file, then the default printer and settings willbe used for the missing entries.

The third line beginning with the keyword HELP is optional as well. It defines a help labelthat will appear on the button labeled with the Method name. It is a string, or more than onestring separated by commas.

GROUPS


GROUPS

Inside the METHOD section is at least one GROUP section. The GROUP sectioncontains one or more EXPERIMENT definitions, and some other optional information. Thissection may seem a bit unnecessary, but when repetition is required (especially over manydifferent samples) it immediately becomes clear that a grouping of experiments is needed.

A GROUP section is defined as follows:

GROUP group_name[USINGTest_Sample][EXECUTE"program_name"][BASENAME"base_filename" mode] IS

EXPERIMENT.....END EXPERIMENT;.[ <more experiments> ]

[PRESENTATION "presentation_file" FORlist_of_box_definitions;

.[ <more presentations> ]]

END GROUP;

The optional USING keyword is followed by a Sample name (defined by aSAMPLE statement described above), or a list of Sample names separated by commas. Thiscauses each experiment in the Group to be run once for each Sample that is specified.

The optional EXECUTE keyword is followed by a single string which is the nameof a Percival program to run when the Group of experiments has all been collected. Thereis a specific parameter passing scheme that must be followed, but this is beyond the scopeof this description.

The optional BASENAME keyword is followed by a single string which isconcatenated with the sample_id and the optional EXTENSION found in theEXPERIMENT declaration to form the filename of the experiment stored on disk. The stringis then followed by a mode indicator. This mode indicator can be either fixed or runtime.See the “Mode Indicator Table” at the end of this description for information on the differentmodes certain parameters may have.


EXPERIMENTS AND PRESENTATIONS

Experiments and Presentations may be defined in any order, mixed or otherwise.However, since Presentations require Experiments to be defined for useful operation, it isrequired that Experiments required for a Presentation must be defined before thePresentation statement. It is a good idea to define all Experiments first, then define allPresentations at the end. Doing this avoids much of the hassle of figuring out where to putthe definitions.

Experiments

Inside each GROUP section is one or more EXPERIMENT declarations and zeroor more PRESENTATION statements. A simple EXPERIMENT declaration is defined asfollows:

EXPERIMENT experiment_name IS[EXTENSIONextension_text][SAMPLE_IDid mode][COMMENT comment_text mode][SLOT slot_number mode][SOLVENT solvent_name mode][TEMPERATURE[temp mode] [ON|OFF mode]][SHIM shim_file_filename][PROCESSINGprocess_list_filename]EXP_FILE experiment_file_filename;

END EXPERIMENT;

The optional EXTENSION keyword is followed by a string which is appended tothe filename of the experiments that will be stored to disk.

The optional SAMPLE_ID keyword is followed by a string which is theidentification string of the experiment. This string forms the first part of the experiment'sfilename. Mode can be any of the three possible modes. Refer to the end of this discussionfor what each mode means.

The optional COMMENT keyword is followed by text which forms the comment/description for the experiment. Mode can be any of the three possible modes. Refer to theend of this discussion for what each mode means.

The optional SLOT keyword is followed by a number indicating which slot to findthe sample in if you have an automatic sample changer. If this is defined as a number butno sample changer is present, this option is ignored. Mode can be any of the three possiblemodes. Refer to the end of this discussion for what each mode means.

The optional SOLVENT keyword is followed by a string which names the solventwhich exists in the sample. Mode can be any of the three possible modes. Refer to the endof this discussion for what each mode means.

EXPERIMENTS and PRESENTATIONS


The optional TEMPERATURE keyword is followed by one or both of the followingtemperature definitions in either order: 1) A universal number with temperature units to setthe temperature value followed by a mode indicator. 2) The keyword ON or OFF to set thetemperature state followed by a mode indicator. Mode may only be fixed or runtime.

The optional SHIM keyword is followed by a string which is the filename of a filethat contains shim information for a spectrometer. Mode may only be fixed or runtime.Refer to the end of this discussion for what each mode means.

The optional PROCESSING keyword is followed by a string or a list of strings whichare separated by commas. Each string is a path and filename of a processing list which theexperiment will be processed with after it has been collected.

The EXP_FILE keyword is a string which is the filename for the experiment filethat will be used to run the experiment.

A more detailed EXPERIMENT has the form like the following:

EXPERIMENT experiment_name IS<all optional parameters as above>EXP_FILE experiment_file_filename DO

parameter_name := parameter_value;..[ <more parameter initializing> ].

TAKE [value comparator] parameter_name[ASSIGN_TO parameter_name] [comparator value][CONSTRAIN multiplier [/ modulus]] [UNITunit_val]..[ <more take_parameters separated by commas> ]

FROM experiment_name;

END EXPERIMENT;

This requires some explanation. Notice the semi-colon at the end of theexperiment_file_filename has been replaced by the keyword DO. This indicates that thereare some extra things we want to define about this experiment. It is possible to initializeexperiment parameters and/or forward parameters from a previous experiment.

First, we can declare and initialize any parameter to any constant value. For example,we may set scans equal to 32 or auto_gain to TRUE with the following statementsrespectively:

scans := 32;auto_gain := TRUE;

Second, we can define that a certain parameter or parameters be taken from a


"previously" defined experiment. In addition, we can specify constraints on the parameter(s)of lower bound, upper bound, multiple of, and modulo of. In the TAKE section, value canbe any constant parameter value. Of course, if it is not a legal value for that particularparameter_name, then maintaining this constraint will fail. Legal comparators are < (lessthan), <= (less than or equal to), > (greater than), and >= (greater than or equal to). It ispossible to define these bound constraints in a number of ways. Here are some examples,including an unbounded parameter:

TAKE x_sweep FROM ...TAKE x_sweep < 2[ppm] FROM ...TAKE 2[ppm] > x_sweep FROM ... (same as above)TAKE 1[ppm] <= x_sweep < 3[ppm] FROM...TAKE 3[ppm] > x_sweep >= 1[ppm] FROM... (same as above)TAKE 3[ppm] > x_sweep, y_sweep >= 1[ppm] FROM...TAKE x_sweep, scans FROM...

It obviously makes no sense to include bounds on the last TAKE statement abovesince the parameters do not have the same type of legal values. However, this is a legalstatement and simply makes no restrictions on the values they may have -- they are justtaken from the experiment specified with their current values.

If it is necessary to constrain the value of a parameter to be a multiple of some numberor the modulo of some number then the CONSTRAIN keyword must be used. After anyand all bounds restrictions, the CONSTRAIN keyword is placed followed by a number thatthe parameter_value will be rounded to be a multiple of. If modulo is desired, include aforward slash next followed by a number for the modulus calculation. If modulus is desired,but no multiplier, a value of 1 (one) must be placed in the multiplier place. For example:

TAKE scans CONSTRAIN 1 / 16 FROM...

This would have the same effect as

TAKE 0 <= scans < 16 FROM...

However if the statement was

TAKE scans >= 0 CONSTRAIN 4 / 16 FROM...

then possible values for scans would be 0, 4, 8, and 12.

To enforce units on a forwarded parameter, use the UNIT keyword. For example:

TAKE x_sweep UNIT [ppm] FROM...

would convert x_sweep to ppm units before passing it to the next experiment. CONSTRAINand ASSIGN_TO can also be used with the UNIT keyword. As in:

TAKE scans >= 10 CONSTRAIN 2 / 100 UNIT [] FROM...

This would enforce scans to be great than or equal to 9, be an even number less than 100,and have no units.

EXPERIMENTS and PRESENTATIONS


It is also possible to forward a parameter from an experiment to a different parameterin the next experiment. This is done with the ASSIGN_TO keyword. Here are someexamples:

TAKE x_sweep ASSIGN_TO y_sweep FROM...TAKE -3[ppm] <= x_sweep ASSIGN_TO y_sweep <= 3[ppm]

FROM...

Both of these commands take the parameter, x_sweep, and applies it's value to y_sweep.The second TAKE command simply adds constraints.

Presentations

As defined above, a PRESENTATION is declared as follows:

GROUP group_name IS..[PRESENTATION "presentation_file" FOR

list_of_box_definitions;.[ <more presentations> ]]

END GROUP;

Notice that Presentation statements are optional. Thus, a Method need not have aplotted output. Of course, the data file will always be saved to disk regardless. Apresentation_file is a path and filename for a presentation template file that was created bythe Presentation Manager tool. To write this section, it requires that one know quite a bitabout what the presentation template file contains. The list_of_box_definitions is exactlythat: a list of box definitions. A box definition can be any of the following types: a namedexperiment, a NULL_DATA keyword, or a NULL_BOX keyword. There is a box definitionfor each box that exists in the template file separated by commas. The first box definitioncorresponds to Box 1 in the template. Likewise the second box definition corresponds toBox 2, etc.

Describing the simplest first, NULL_BOX is a keyword indicating that a data fileis not a parameter to this template for the box number of its position. Thus, if Box 1 in thePresentation template file is not a parameter box, then NULL_BOX would be the first boxdefinition.

NULL_DATA indicates that this box is indeed a parameter box, but no data file willbe passed to it. It is necessary to place a number in brackets immediately in front of thiskeyword (leaving no spaces) to indicate the number of the parameter that this will go into.For example, [2]NULL_DATA indicates that there will be no data file passed as the secondparameter.

A named experiment consists of a number in brackets (like was done forNULL_DATA) followed immediately by the experiment_name. The number in brackets,


as above, indicates which parameter will get this data file. If the user would like to displayprocessed data, then immediately following the experiment_name (leaving no spaces) placea @_ followed immediately by an INTEGER which is an index into the list ofprocessing_lists. For example, to place a processed data file using the second processinglist into the fourth parameter of the template file one would write: [4]Exp_Name@_2

*** FILENAME NOTE ***

An experiment's filename (the name that the collected data will be saved to) iscreated from three components. First, the SAMPLE_ID from the EXPERIMENTdeclaration, followed immediately by the BASENAME that is in the GROUP section, andfinally followed by the EXTENSION taken from the EXPERIMENT declaration. The datafile will also be assigned a version number.

Mode Indicator Table

A mode indicator can be one of the following: fixed, runtime, or sample. Refer tothe following table for descriptions of each.

FIXED A fixed mode indicator means that the value of that parameter cannot be changedwhen the experiment is run. This will be the case for Methods defined as NOTbeing an Advanced Method.

RUNTIME A runtime mode indicator means that the value of that parameter may be changedjust prior to submission given that the Method being submitted is an AdvancedMethod.

SAMPLE A sample mode indicator means that the value of that parameter will take on thevalue(s) that is (are) defined in the “Use Sample(s)” parameter box for thatGroup. This will be the case regardless of the Advanced mode. The experimentwill be run once for each sample.

Logic of Flow in the Automation Editor


LOGIC OF FLOW IN THE AUTOMATION EDITOR

When the user first starts the Automation Editor with no automation template to loadat start-up, the user is presented with a blank screen. Before any Experiments may be addedto the file, a title for the Method must be supplied. The Group will automatically be titledwith the same name as the Method, but the user may change either title. Following theseone or two steps, Experiments may then be defined.

It is recommended that you create any Sample definitions first, followed by creatingthe Experiments, and lastly supplying Presentation information. It is not necessary to definethe Samples first, but it is required that Experiments be defined before Presentations. It ispossible to define Experiments that do not have Presentations (no printer output), but notvice versa.

In a basic Method, the only necessary line to fill in (besides the Method, the Group,and the Experiment titles) to define an Experiment is the Experiment File line. Without anexperiment file, the experiment cannot run. Every experiment in every Group will be runonce on the Spectrometer. If Samples are used in the Group, i.e. the Use Sample(s) fieldhas one or more Sample titles in it, then only the experiments in that Group will be run oncefor each Sample specified.

Parameters can be initialized for any Experiment and they may only be initializedto constant values. For example, you CANNOT define the following:

filter_start := 1[ppm];filter_stop := filter_start + 1[ppm];

In this case, filter_start will be set correctly, but filter_stop will be set to the string"filter_start + 1[ppm]". Obviously not what was intended. You must specify the aboveinitialization as:

filter_start := 1[ppm];filter_stop := 2[ppm];

Forwarded parameters may only come from a previously defined Experiment. Theorder in which the Experiments appear in the list box is the order in which they will run onthe spectrometer. In a way, Forward parameters are like Initialize parameters except thatthey get their initial values from an experiment rather than from a constant user set value.

DELTA User’s Guide, v 3.2 G-1

APPENDIX G: PRESENTATION MANAGER AND

TEMPLATE FILE FORMAT

CONSOLE COMMANDS

A unary operator called ‘pm’ does the bulk of Presentation Manager’s work. It is possibleto call pm from processing lists, the command line, and percival code to aid in theautomation of plotting. The following is a description of how to call pm.

The Presentation Manager kernel is an operator called ‘pm’. To facilitate the automation ofplot output, this operator can be called from the command line, a percival program oroperator, or a processing list. There are four execution modes associated with pm.Execution mode 1 is for executing a template file, 2 is for reading a template file, 3 is forexecuting symbolic information, and 4 is for writing symbolic information to a templatefile.

pm 1: template_file :: VT_FILE [: runtime_files :: (VT_FILE, VT_SET) [:plot_parameters :: VT_SET ]]

pm 2: template_file :: VT_FILE

pm 3: symbolic_info :: VT_SET : plot_parameters :: VT_SET :preview_boolean :: VT_BOOLEAN

pm 4: symbolic_info :: VT_SET : template_file :: VT_FILE

The runtime files in execution mode 1 correspond to parameter numbers specified in thetemplate file. These numbers are designated in file variables, and appear in the form P#,where # is the number of the file that will be referenced from the runtime_files set. Forexample, if file1 in a template file references parameter 3, then runtime_files should beat least a three element set, and file1 refers to the third element in that set. If only oneparameter number is specified in the template, then runtime_files may be a file insteadof a set of files.

The plot_parameters argument in execution modes 1 and 3 should be of the form:

[queue :: VT_BOOLEAN, delete_file :: VT_BOOLEAN, file_name :: VT_STRING,plotter :: VT_STRING, paper_size :: VT_STRING, color :: VT_BOOLEAN,output_orientation :: (WM~LAND|WM~PORT), tesselation_value ::VT_NUMERIC}

For execution mode 1, if no runtime files are to be specified, but plot_parameters isgoing to be specified, an empty set should be placed as the second argument.

For execution mode 3, if plot_parameters is not going to be specified, then an empty set

G-2 DELTA User’s Guide, v 3.2

should be used in its place.

The symbolic_info argument referred to above should be of the form:{{position :: VT_SET, type :: VT_STRING, features ::VT_SET, attributes :: VT_SET,data :: VT_SET, processing_list_file :: VT_STRING,ruler_info :: VT_SET}...}

A sample template File (.pmt)

The following sample file describes a single, full-size box. The ‘geom’ indicates that thisbox will display data. The empty sets indicate that defaults are to be used for features andattributes.

[box]box1: {0[%], 0[%], 0[%], 0[%]} : ‘geom’ : {}:{}

[file]file_1 : ‘/usr/files/data/1d/1heb.1’

[process_lst]process_lst_1 : ‘/usr/files/process_lists/reverse.lst’

[transformation]file_1 => process_lst_1 => box1

[ruler]box1: X : 100 : 0

[end]

The file variable file_l is assigned a literal string, referring to a data file called 1heb.1.

The processing list variable process_lst_1 is assigned a processing list file calledreverse.lst.

The transformation section specifies that file_1 is to be processed usingprocess_lst_1, and then displayed in box1.

The ruler section indicates that box 1’s x-ruler will be set to 100 at the upper bounds, andto 0 at the lower, in whatever units the file is in.

Comments may be placed in the template files. Any text following ‘--’ will be ignored.

DELTA User’s Guide, v 3.2 H-1

APPENDIX H: TERMINAL CONSOLE PROGRAM

The terminal console program allows you to communicate remotely to Delta through aterminal emulator. This allows you to remotely monitor spectrometers without a SiliconGraphics terminal. This feature is useful when you are running a lengthy experiment, or aseries of experiments. It allows you to see what jobs are running, and to cancel a job ifneed be.

Note: The terminal console program requires that a copy of Delta be runningon the workstation. The terminal console program will only connect to Deltawhen it is run from the same UNIX account that started Delta. The copy ofDelta running on the workstation does not need to be connected to aspectrometer; you make the necessary spectrometer connections from theterminal console program.

For help on console, type:$ console -h

To start the program, type:

console [-r] [-l] [-e] [-w] [-p init_mode] [-n name] [- s number] [-h hostname]

with or without any of the optional flags which are in brackets.where-r : Resets all client message ids and manages message passing-l : Lists all available servers-s : Selects a server by number-e : Line editor enabled (Default)-w : Without line editor enabled-p : Initial prompt mode, specifying mode of input-n : Requests connection by name-h : Connects to host

Once a console program is running and connected to Delta, type:x_con to connect to the nongraphical spectrometer connection tool that has most of thesame functions as the Delta Spectrometer Control Tool. This tool allows you to dothe following (for clarification, see the discussion in Chapter 4):• connect, disconnect or monitor a spectrometer• access information on spectrometers and ascertain which spectrometers are free• supply a password• scroll the list of connected spectrometers• show jobs• abort a job or an entire queue

H-2 DELTA User’s Guide, v 3.2

• start a job.

The screens below illustrate the menu of choices described above:

DELTA User’s Guide, v 3.2 I-1

APPENDIX I: TOOL ICONS

Delta tools, when turned into icons, have identifiable and distinguishable pictures to helpyou rapidly pick them out from the array on your screen.

Icon Tool


Presentation Manager template

Pick tool

Phase 2D

Parameter tool

Get directory

I-2 DELTA User’s Guide, v 3.2

Delta console

Interactive base correction

Geometry tool

Console manager

File Math

Export

Import

Experiment tool

Icon Tool


Reference

Dept/Inept

Calculator

Debugger

Data slate

T1 Analysis

Automation

Autoqueue

Icon Tool


Automation Editor

Connect

Chart

Cursor

Level

Automation

Line Editor

Parameter Editor

Icon Tool


Preferences

Connection

Spectrometer

Spread Sheet

Signal/Noise

View Control

Transfer Integral

Icon Tool


Peak List

Parameter Viewer

3D Plotter

Widget Editor

Template

Window Phaser

1D Processor

Icon Tool


nD Processor

Process

Icon Tool

DELTA User’s Guide, v 3.2 J-1

APPENDIX J: UNIX AND VI COMMANDS

This appendix lists Unix and VI commands frequently used in conjunction with runningDelta.

I. UNIX COMMANDS

Command Usage Example

pwd pwd Lets you know your present working directory; i.e., if you are in the delta account it will printout/usr/people/delta.

clear clear Clears the screen.

cd cd .. Changes directory to next higher directory in tree,cd .. when presently in /usr/people/delta results in the new directory being /usr/people cd.

cd cd [path] cd /usr/people/delta/files/data changescurrent directory to/usr/people/delta/files/data.

cp cp [from] [to] cp /usr/people/delta/filename.x/usr/people/delta/files/data/,copies filename.x from /usr/people/delta/to /usr/people/delta/files/data.

mv mv [from] [to] mv /usr/people/delta/filename.x/usr/people/delta/files/data/,moves filename.x from /usr/people/delta/to /usr/people/delta/files/data.

rm rm [filename] rm filename.x removes filename.x from thecurrent directory. Wildcarding is supported,i.e., rm file* removes all files that have the name file.

df df -k Displays disk space in kilobytes.

ls ls -la Lists all files including hidden files. Hidden files have theformat .filename (period before filename).

ls ls -ltr Lists files by date in descending order.

J-2 DELTA User’s Guide, v 3.2

tar cv tar cv * Tape archival of files from disk. Files in the currentdirectory and all sub directories are archived.

tar rv tar rv * Tape archival with append. Files can be appended topreviously archived files using the tar cv command.

tar xvtar xv [filename]Extracts files from tape back to disk. Withoutan argument all files are restored. A filename argumentrestores a specific file.

tar t tar t Lists contents of a tape made using tar.

ls > test.txt ls > [filename]">" stands for pipe. Normally ls wouldlist files on the CRT. By using “>” the file listing is“piped” to a diskfile. A filename must be supplied.The “pipe” can be used in all cases when an output is being generated.

mkdir mkdir [directory name]Creates a subdirectory.

II. VI COMMANDS

Command

x Deletes a single character.

i Inserts. Must be followed by an escape key stroke to exit insert node.

a Appends to the end of a line. Must be followed by an escape key stroke.

: Starts command line. Before the wq! and q!

wq! Writes the current file and quits.

q! Quits VI without saving the changes.

DELTA User’s Guide, v 3.2 K-1

APPENDIX K INSTALLING JEOL AUTOTUNE PROBES

This appendix describes the procedures for installing JEOL AutoTune probes on EclipseNMR spectrometers.

1. Turn off the spectrometer power.2. Connect AutoTune controller box to B-Bus. This may be done directly to the

spectrometer motherboard or in series with the sample changer. DO NOT connect thespeedometer cables to the probe.

3. Plug the Autotune controller into 120V; there may be two 120V plugs.4. Power on the spectrometer, acquisition system, and AutoTune controller (two

switches). The system should come up as normal. Login and run Delta.5. Open a terminal shell and login into the acquisition system as root.6. If the AutoTune probe is being installed for the first time, the 2564.probe file must be

checked for the correct entries. For each nucleus the COARSE, TUNE and MATCHvalues must be verified. After running the specifications, you should have writtendown values for 1H, 13C, 31P, and 15N. If other nuclei are desired, the probe must bemanually tuned to the nucleus and the values entered in the 2564.probe file beforeautomatic probe tuning is attempted.

Write the values here: Nucleus - COARSE - TUNE - MATCH

1H - HF19F - HF31P13C15N

7. Type cd /eclipse/probes8. Type ls The files for the standard TH5 autotune probe (probe id 2564) are:

2564.shims 2564.probe 2564.limits 2564.dials

The .shims and .probe files should already exist. If they do not exist - STOPnow - you have not installed the probe correctly. The .limits file may exist but must be verified before installing the autotune probe. The .dials file should not exist yet.9. Edit the 2564.probe file with vi and place the recorded COARSE, TUNE and MATCH

values for the nuclei in the correct domain sections. Save the file and exit vi. You mayhave received a printout of a probe file with the probe. Do not assume those numbersare correct, every nucleus must be verified in installation by manually tuning theprobe.

10. The 2564.limits file must be verified. On the probe, turn the LF TUNE, LF MATCH,HF TUNE, and HF MATCH knobs to their minimum values. Write these numbers

K-2 DELTA User’s Guide, v 3.2

down. Turn the same knobs to their maximum values and write the numbers down.DO NOT FORCE THE DIALS. As soon as there is any turning resistance, theend has been reached.

LF TUNELF MATCHHF TUNEHF MATCH

11. Edit the 2564.limits file to match these verified limit values. Change the values inthe file to match the measured values. If the file does not exist, create a file with vi.After editing the file, save it to disk and exit vi.

The format of the .limits file is:LF TUNE minimumLF TUNE maximumLF TUNE step size (default 10)LF MATCH minimumLF MATCH maximumLF MATCH step size (default 10)HF TUNE minimumHF TUNE maximumHF TUNE step size (default 10)HF MATCH minimumHF MATCH maximumHF MATCH step size (default 10)

For example: 150 4500 10 200 2800 10 150 1100 10 160 2750 10

12. Connect the cables to the Autotune probe. There are 5 cables LF COARSE, LF TUNE,LF MATCH, HF TUNE, HF MATCH. These are color-coded on the collar. You mayneed to gently jiggle the knobs to engage the worm gears. Be careful, don't force thegears.

13. Connect to the instrument via Delta in Console mode.14. From the spectrometer control window, select the PreTune button,15. Fill in the blanks on the screen by reading the dial values. Make sure you get the order

correct, and do not assume they are where you left them because they will changewhen the cables are connected.

Probe Tuning

DELTA User’s Guide, v 3.2 K-3

16. Save the .dials file by clicking the button. A message should be displayed in theMaster Console.

17. Unlink from the spectrometer and reconnect as normal.18. Submit a single_pulse proton experiment. Watch closely in the Master Console,

messages regarding tuning will be displayed.19. If all is well, the probe will initialize itself by checking the 31P tuning. This is how it

finds the COARSE position (X, A, B, C, D). If there is an error, a message will beprinted in the Master Console. The most common error is “Dials file not found.” In thiscase, re-connect as console and save the dials file again, then re-boot the acquisitionunit. The presence of the dials file can be verified by rlogging into the acquisitionsystem and looking in /eclipse/probes. To prevent damage to the probe, the dials file isdeleted while the probe tuning is in motion. Therefore it may appear and disappear.

20. After initialization, the probe will tune for the requested nucleus in the experiment, inthis case 1H.

21. The probe should reinitialize itself properly each time, if there is a dials file present. Ifno dials file is found, a message will appear in the Master Console, and the systemmanager must create a new dials file with the PreTune button.

PROBE TUNING

Probe Tuning is performed using the probe_tune experiment in the globalexperiments directory. The probe_tune experiment uses very low power RF and adirectional coupler to adjust the probe tuning.

❏ To tune a probe:1. Load the probe_tune experiment from the global directory.2. Set the desired nucleus for tuning, and submit the experiment.3. If you are tuning a current generation probe with digital tuning readout, find the tuning

sheet for the probe and dial in the standard values for the nucleus you are tuning. Ifyou are tuning the broadband channel, find the correct tuning capacitor stick on thesheet and insert the capacitor into the probe.Note: make sure that any existing capacitor sticks are removed from the probe if theyare not required.

4. Using the level knob and the x10 button, bring the meter to 50% scale.5. Use the Tune knob to minimize the meter deflection. The Tune knob will be different

for the HF and LF channels. On some probes, the HF Tune is a small red knob withouta digital readout. The LF tune is usually a digitally encoded knob. Be certain you areturning the correct knob.

6. If the meter deflection decreases to a value too small to see on the meter, use the levelknob or x10 button to increase the deflection.

7. When a minimum is found with the Tune knob, move to the Match knob, if there isone for the channel you are tuning. Not all probes have Match knobs for all channels.If the probe channel you are tuning does not have a Match knob, move the Match knobto find a minimum on the meter. Now that you are at the minimum, move the Matchknob one direction to increase the meter deflection. Remember the direction you

K-4 DELTA User’s Guide, v 3.2

turned the knob!8. Turn the Tune knob to minimize the deflection again. If the new minimum deflection is

lower than the previous minimum deflection, then the Match knob was moved in thecorrect direction. If the new minimum deflection is higher than before, then the Matchknob was moved in the wrong direction.

9. Continue this process iterating between the Tune and Match knobs until the bestminimum is found. As a general rule, a clockwise movement of the Tuning capacitorswill tune to a higher frequency.

10. If this is the first time the probe is being tuned to a nucleus, write down the Tune andMatch values on the tuning sheet or roadblock.

11. Terminate the probe_tune experiment from the spectrometer queue.

Before running an NMR experiment on an Eclipse system, confirm that theBNC cables are correctly connected. Running an NMR experiment with thecables left in the probe tuning configuration will damage the directionalcoupler.

DELTA User’s Guide, v 3.2 L-1

APPENDIX L: DELTA V3.2 SOFTWARE INSTALLATION AND

CONFIGURATION INSTRUCTIONS

This appendix describes the procedures for installing and upgrading the Delta software andthe Eclipse control software, and for setting up new user accounts.

Portions of this document contain Year 2000 information and is covered by the FederalYear 2000 Readiness and Disclosure Act enacted October 19, 1998, for more informationplease contact your local JEOL office. JEOL USA Year 2000 compliant products are pro-vided under the standard JEOL USA terms and conditions of sale, license, and support.

I. SYSTEM REQUIREMENTS FOR DELTA V3.2

Delta V3.2 supports several additional workstation and acquisition systems. These areoutlined below, for more information please contact your local JEOL office.

Workstations:

SGI - IRIX:See sections III and IV for installation or upgrade instructions.

Indy R4xxx, R5xxx - any graphics levelIndigo R4xxx - XS, XS24, XZ or Elan graphicsIndigo2 R4xxx, R5xxx- XZ, Extreme, or Impact graphicsO2 R5xxx, R10K - any graphics levelOctane - any graphics levelAll systems with minimum 64 Mbyte RAM (128 Mbyte for O2 & Octane)Either IRIX 6.2, 6.3 and 6.5.x operating system on the workstation.Note: Version 3.2 is not supported for IRIX 5.x and earlier on the workstation.CD-ROM driveNote: SGI IRIX 6.2 and 6.3 require Y2K patches, to obtain a the Y2K patches for SGIRIX version 6.2 o 6.3 please contact JEOL.

Intel - LinuxSee sections V and VI for installation or upgrade instructions.

Intel Pentium II, 400 MHz or fasterRedHat Version 6.2 LinuxXFree86 V3.3.5 or Xi Graphics V1.1 3D Accelerated-X Drivers256 Mbyte MemoryEthernet Network card for license key.CD-ROM driveNote: JEOL has tested the following configurations: Pentium II-450, Pentium III-733,Pentium III-800, with Evans & Sutherland Lightning 1200, Matrox G400, 3DlabsOxygen GVX1, 3Dlabs Oxygen VX1, ATi Radeon 64MB.Note: Please contact JEOL to discuss Linux system configurations and performancelevels.

L-2 DELTA User’s Guide, v 3.2

IBM - AIXSee sections VII and VIII for installation or upgrade instructions.

IBM RS/6000 Power PC workstations with 24 bit graphicsAIX Version 4.3.2 or 4.3.3 with the latest patches256 Mbyte MemoryCD-ROM driveNote: JEOL has tested the following models: 140, 150, 260 with GXT 550, GXT2000, GXT 3000 Graphics Boards

Sun - SolarisSee sections V and VI for installation or upgrade instructions.

Sun UltraSPARC 10 workstations with 24 bit graphicsSolaris Version 8 with OpenGL, October 2000 release256 Mbyte MemoryCD-ROM driveNote: JEOL has tested the UltraSPARC 10 with Creator 3D, Elite M3 and PGX 24graphics boards.

Delta V3.2 uses the same software license key as previous versions of Delta, if you areupgrading you do not need a new key for Delta.

Acquisition Systems:Delta V3.2 supports all acquisition systems with the SGI Indy computer running SGIIRIX V5.3. Version 3.2 is not supported for SGI V35 acquisition systems runningIRIX V4.0.5, however Delta V3.2 will communicate with and run experiments onV3.1.2 V35 based acquisition systems. To update the acquisition system to DeltaV3.1.2 please see section IV-c after installing Delta V3.2.

NMR Spectrometers:Delta V3.2 supports the following NMR spectrometer hardware:Eclipse+ NMR spectrometerEclipse NMR spectrometerDelta Upgrade for GX, GSX, CPF, EX and Lambda spectrometers

Delta V3.2 is installed from CDROM using the SGI Software Manager tools or installscripts for the Linux, AIX, and Solaris versions. Please find the appropriate section toinstall Delta on your system.

II. PREPARING FOR THE DELTA V3.2 SOFTWARE INSTALLATION ORUPGRADE

Note! Check the system requirements for your systembefore attempting to install Delta.

III. Installing or Upgrading the Delta Software on SGI IRIX Systems


The Delta software package for processing NMR data is supplied on CDROM. The instal-lation tools will install Delta into /usr/delta/.

The Delta Software CDROM contains: the Delta NMR Processing Software, Standard Ex-ample NMR Data for Delta, the Delta Software Manuals in Adobe Acrobat (PDF) format,the Adobe Acrobat Reader V4.0, and several shareware PC / MAC programs that we havefound useful. The PC and MAC programs are supplied as a courtesy without warranty orsupport. The manuals on CDROM can be accessed by opening the CDROM desktop folderand clicking on the appropriate icon.

General notes: Delta requires Netscape Navigator and Adobe Acrobat Reader to accessthe help files. Netscape Navigator must be installed before installing Delta. Adobe Acro-bat Reader is also required to view and print the Acrobat format manuals on the CDROM.The Adobe Acrobat Reader can be installed as part of the Delta installation procedure.

When installing Delta for the first time you will need to have a permanent Delta LicenseKey. To obtain a Delta License Key install Delta and type /usr/delta/global/verify to list the Delta Machine ID for new installations. Fill out the Delta License Keyrequest form and FAX the form or e-mail the information to JEOL USA, Inc. You shouldreceive a permanent Delta License key back within 2 weeks.

The Delta software has a 60 day grace period from the time of manufacture before it willcheck for the Delta License key. Copies of Delta delivered after the 60 day grace periodshould include a 60 day temporary Delta License key.

Important! Please read the release notes for Delta V3.2 before starting the in-stallation. Instructions to access the release notes are in the CD booklet.

Note: Please read and understand all instructions before starting installation.

Note: The steps for installing Delta or upgrading the acquisition system are out-lined below. Bold text is to be entered by the user. Bold text indicates a buttonor menu option that the user is to select. Click indicates a mouse action. Enter↵at the end of each line is assumed unless stated otherwise.

III. INSTALLING OR UPGRADING THE DELTA SOFTWARE ON SGI IRIXSYSTEMS

There are 6 major parts to the complete Delta NMR software package for SGI IRIX sys-tems:


1. Login to the system(root) account.2. Insert the Delta Software CDROM into the CDROM drive.3. Double Click on the CDROM icon to open the desktop CDROM Folder.4. Double Click on the Install_Delta icon to start the SGI Software Manager.5. The Software Manager window will now appear.

Note: Only the Software products and Software subsystems selected with thered check mark in the Install buttons will be installed.

6. Click on the Custom Installation Button.7. Click on the Install button for the Delta Software License type that is correct for

your system. The Delta NMR Data Processing Package and the Delta (NodelockLicense) software are installed by default. Turn off the Delta (Nodelock License) ifyou are installing the Delta (Network License).

Note: Only the Delta (Nodelock License) or the Delta (Network License) willinstall. Swmgr will generate a conflict if you try to install both subsystems.

Note: The Delta (Network License) software will not work with Delta(Nodelock License) keys.

8. Click on the Install button for the Delta [v32] Eclipse Software for IRIX if you havean Eclipse or Delta-Upgrade NMR Spectrometer Acquisition system. Choose the IRIXversion (IRIX 4.0.5 or IRIX 5.3) that is correct for your acquisition system.

9. Click on the Install button for Adobe Acrobat Reader if Adobe Acrobat is notinstalled on your system and you want to view the Acrobat Format files on the

Table N-1: Delta NMR software package components

Component Name Description InstallationStatus

Delta Webserver Delta Web interface to submit experiments optional

Delta [v3.2](Network License)

Floating network Delta Software license.Requires a special license key.

optional

Delta [v3.2] (Nodelock License)

Standard Delta node locked software license. standard

Delta [v3.1.2)]Eclipse Software forIRIX4

IRIX v4.0.5 files for Eclipse and Delta-UPGNMR spectrometer computers. This is the Del-ta V3.1.2 kit.

optional

Delta [v3.2)]Eclipse Software forIRIX5

IRIX v5.3 files for Eclipse and Delta-UPGNMR spectrometer computers.

optional

Delta [v3.2] NMR DataProcessing Package

Support files necessary for the Delta NMRSoftware package to operate correctly.

requiredstandard

IV. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from an SGI Workstation


CDROM or use the Delta help files.10. Click Start to begin the Delta Software installation.11. The SGI Software Manager will now install the Delta software sub-systems selected.

The install process will also identify any running Eclipse or Delta-Upgrade NMRspectrometers and set up an .rhosts file in the guest account, if the guest account ispresent, or in the root account, if the guest account is not present. The .rhosts file isused to install software on the acquisition system computer.

12. After the software installation has completed click OK to acknowledge the completionof the installation process.

13. Click File/Quit on the pull down menu or type <Ctrl>Q in the Software Managerwindow to exit the swmgr program.

14. Close the CDROM folder.15. Right Click on the CDROM Icon and select Eject CDROM.16. Put the CDROM in a safe place for future use.17. Follow the instructions included with the Delta License Key to install the Delta

License key, if one is not already installed.18. If you have an Eclipse+, Eclipse, or Acquisition System attached to your system,

continue with section IV Upgrading an Eclipse+, Eclipse or Delta-UpgradeAcquisition System.

IV. UPGRADING AN ECLIPSE+, ECLIPSE, OR DELTA-UPGRADEACQUISITION SYSTEM FROM AN SGI WORKSTATION

For Eclipse+, Eclipse or Delta-UPG Acquisition Systems with Delta Currently In-stalled Only!

The steps to upgrade the acquisition system software are outlined below.A. Setup for Eclipse+, Eclipse, or Delta-Upgrade Acquisition software upgrade.

1. Upgrade the Host workstation as described above in section III.2. Login to the system(root) account on the workstation, and create a terminal

window.3. cd /usr/delta/eclipse to change to the eclipse software directory on the

workstation.4. ./backup_spectrometer eclipse2 to start the configuration file backup

script. The backup_spectrometer script will copy all acquisition configuration filesto the workstation.

5. Enter the root password for the acquisition system.6. The acquisition system configuration files on the acquisition system will now be

copied to the workstation.7. rlogin root@eclipse2 to login to the acquisition system computer.8. uname -r, to list the version of IRIX.9. For Irix 5.3 go to step B, for Irix 4.0.5 go to step C

B. For SGI IRIX v5.3 Indy based systems, follow this procedure:1. /etc/init.d/local stop to stop the eclipse and control software

programs.2. inst -f eclipse1:/usr/delta/eclipse/dist to start the install


software and use the Delta workstation directory /usr/delta/eclipse/dist as thedistribution directory. This uses the default account guest on eclipse1 to access thedirectory.

3. go to start the software install process. The system will now install the updatedversions of acquisition control programs and configuration files.

Note: If a network error or login error occurs then quit, and try step 2. againusing the command inst -f root@eclipse1:/usr/delta/eclipse/dist.

4. quit to exit the install software.5. init 6 to reboot the acquisition system. The spectrometer will reboot and start

the Delta control process for IRIX V5.3.

C. For SGI IRIX v4.0.5, V35 based systems follow the following procedure:Note: Delta V3.2 will communicate with Delta V3.1.2 SGI V35 IRIX 4.0.5based acquisition systems. If you are upgrading from a version prior to V3.1.2plase upgrade the acquisition system to Delta V3.1.2.

Note: Delta V3.1 is the last version of Delta that will support the SGI 4.0.5 Ac-quisitions systems. SGI IRIX 4.0.5 has significant Y2K problems with February29, 2000, please contact JEOL for more information.

1. killall eclipse control to stop the eclipse and control softwareprograms.

2. exit to return to the workstation.3. cd /usr/delta/eclipse to change to the eclipse software directory on the

workstation.4. ./update_spectrometer eclipse2, this script will ask for the acquisition

system root password twice.5. Enter the root password for the acquisition system to upload the acquisition system

configuration files.6. Enter the root password for the acquisition system to copy the updated

configuration files back to the acquisition system. The new programs for theacquisition system will also be copied to the acquisition system.

7. rlogin root@eclipse2 to login to the acquisition system computer.8. init 6 to reboot the acquisition system. The spectrometer will reboot and start

the Delta control process for IRIX V4.0.5.

V. INSTALLING OR UPGRADING THE DELTA SOFTWARE ON INTEL LINUXOR SUN SOLARIS SYSTEMS

1. Login to the system(root) account.2. Insert the Delta Software CDROM into the CDROM drive.3. When the CD disk browser opens click on install_delta to start the Delta install

script.4. Type a letter or number to change the install defaults as appropriate for your system.

VI. Upgrading an Eclipse+, Eclipse, or DELTA-Upgrade Acquisition System from Linux, or Solaris.


5. Type P to proceed with the installationNote: The Delta (Network License) software will not work with Delta(Nodelock License) keys.

6. When the installation is finished close the terminal window if it does not closeautomatically.

7. To eject the CDROM on Intel Linux systems close the browser window, right click onthe CDROM icon and select eject. To eject the CDROM on Sun Solaris systemsselect Eject from the File menu on the browser window.

8. Put the CDROM in a safe place for future use.9. Follow the instructions included with the Delta License Key to install the Delta


continue with section VI Upgrading an Eclipse+, Eclipse or Delta-UpgradeAcquisition System.

VI. UPGRADING AN ECLIPSE+, ECLIPSE, OR DELTA-UPGRADEACQUISITION SYSTEM FROM LINUX, OR SOLARIS.

1. Login to the system (root) account.2. Insert the Delta Software CDROM into the CDROM drive.3. When the CD disk browser opens click on spectrometer_install to start the Delta

acquisition software install script.4. Answer the questions as appropriate for your system.5. Execute the requested command on the acquisition system. Typically "cd /var/

tmp; sh eclipse.shar".6. Reboot the acquisition system by typing reboot and answer Y if necessary.7. The acquisition system will automatically log the user out of the system as the system

reboots.8. Close the terminal if it does not close automatically.9. To eject the CDROM on Intel Linux systems close the browser window, right click on

the CDROM icon and select eject. To eject the CDROM on Sun Solaris systemsselect Eject from the File menu on the browser window.

10. Put the CDROM in a safe place for future use.11. When the spectrometer reboot completes the spectrometer is ready for use.

VII. INSTALLING OR UPGRADING THE DELTA SOFTWARE ON IBM AIXSYSTEMS

1. Login to the system(root) account.2. Insert the Delta Software CDROM into the CDROM drive.3. Open a terminal window.4. Type mkdir /cdrom, to create a directory for the CDROM. Note: Ignore any

messages about the directory already being present.5. Type mount -0 ro -v cdrfs /dev/dco /cdrom to mount the CDROM

drive.


6. Type /cdrom/install_delta to start the install script.7. Type a letter or number to change the install defaults as appropriate for your system.8. Type P to proceed with the installation

Note: The Delta (Network License) software will not work with Delta(Nodelock License) keys.

9. Type umount /cdrom to unmount the CDROM drive.10. To eject the CDROM press the eject button on the CDROM drive.11. Put the CDROM in a safe place for future use.12. Follow the instructions included with the Delta License Key to install the Delta


continue with section VIII Upgrading an Eclipse+, Eclipse or Delta-UpgradeAcquisition System.

VIII. UPGRADING AN ECLIPSE+, ECLIPSE, OR DELTA-UPGRADEACQUISITION SYSTEM FROM AIX.

1. Login to the system (root) account.2. Create a terminal window.3. Insert the Delta Software CDROM into the CDROM drive.4. Mount the CDROM on AIX systems with mount -0 ro- v cdrfs /dev/dco

/cdrom .5. Type /cdrom/spectrometer_install to start the spectrometer install script.6. Answer the questions as appropriate for your system.7. Execute the requested command on the acquisition system if necessary. Typically "cd

/var/tmp; sh eclipse.shar".8. Reboot the acquisition system by typing reboot and answer Y if necessary.9. The acquisition system will automatically log the user out of the system as the system

reboots.10. Close the terminal if it does not close automatically.11. Type umount /cdrom to unmount the CDROM drive.12. To eject the CDROM press the eject button on the CDROM drive.13. Put the CDROM in a safe place for future use.14. When the spectrometer reboot completes the spectrometer is ready for use.

IX. USER ACCOUNT SETUP

1. Login to the system (root) account.2. Create a user account with the name delta using the system management tools for the

workstation. This is typically /usr/people/delta/. This account is where theuser runs Delta, and where the user's raw data, Delta NMR data, and program sourcesare kept. Select the “tcsh” for user shell if available. This shell provides command lineediting, a history of commands, command completion and many other convenient userfeatures.

3. Create a terminal window.

IX. USER Account Setup


4. Type login delta to log in to the account created for Delta from a terminalwindow, and create a terminal window.

5. Type /usr/delta/setup/copy_setup will copy several files to the localdirectory to allow Delta to be run.

Caution: this will copy the following files to *.O versions and copy new filesto the directory: .auxchestrc, .chsrc, .grosview, .login,.icons/login.icon, .delta_configure and.delta_parameter_list

6. Logout of the workstation completely.7. Login to the account created for Delta.8. Create a terminal window.9. Type delta -v -n in the terminal window. This should print out the version

information for Delta.10. Delta is now ready to use. Type delta in a terminal window to start the Delta NMR

software program. Note: some operating systems may have a menu or desktop icon tostart Delta in addition to the command line.

Note: For SGI systems on the Toolchest under Desktop/Customize/Windows set “Save Windows & Desks:” to Explicitly, click Set HomeSession, and click Close. This will prevent multiple copies of Deltastarting if the user logs out of the workstation with Delta running and “Save

Windows & Desks:” set to Continuously.

DELTA User’s Guide, v 3.2 M-1

APPENDIX M: X WINDOWS EMULATION

X emulation is a process that initiates a Server-Client relationship between the PC/Macand the Silicon Graphics workstation over a local area network (LAN).

SGI IRIX setup:The SGI workstation needs to have the X Display Manager (xdm) active. To determine ifxdm is active, open a UNIX shell on the SGI and type chkconfig. There should be an entryxdm with a value on or off. If it is off, follow the procedure outlined below.

login root Supply the root password.chkconfig xdm on This will turn xdm on.init 6 Restart the workstation

X-Server Requirements for PC or MAC:

System Memory 64Mb

Video Memory Minimum 8Mb

Screen Resolution Minimum 1024x768

Network TCP/IP

Input or Keyboard map file Supplied by JEOL (see below). These arelocated in the

/usr/delta/setup/ directory on the SGIworkstation.

Communication Configure for XDMCP-query, thisrequires specifying the name or IP addressfor the SGI workstation.

Protocol Use the defaults that are standard with thesoftware package.

Screen Definition: Single window mode.

Video Characteristics: True color representation.

Fonts 100, 75 and Misc. DPI fonts. The fontsshould appear in this order for the bestresults.

M-2 DELTA User’s Guide, v 3.2

PC X-Servers:

Exceed by Hummingbird Communications, www.hummingbird.com:After installing the software, place exceed_delta.kbf file in the user directory underthe Exceed program directory. Using the configuration tool select exceed_delta.kbf as thedefault keyboard map.

Reflections by WRQ Inc., www.wrq.com:After installing the software, place wrq_delta.kbf file in the user directory under thereflections program directory. Using the configuration tool select wrq_delta.kmp asthe default keyboard.

MAC X-Servers:

Exodus by White Pine Software Inc., www.wpine.com:• After installing the software, place exodus_delta.bin in the Extras directory.

Using the configuration tool in Exodus select exodus_delta.bin as the defaultkeyboard.

Notes:

• The X-windows mode of operation with Delta only works with the node locked Deltalicense.

• Multiple users on an SGI workstation will impact the overall performance. Up to 3users on an SGO O2, 180SC, 128 MB system can be supported for 1D and small 2Dwork.

• Delta can run on a large SGI server; for example, Challenge-L or Origin 2000.• The X-Windows performance is most strongly determined by the PC or MAC and the

graphics card used for display.

Delta User’s Guide, v3.2 Index-i

Index

Numerics1 files E-71D Processor 5-2, 5-4, I-6

Extended Mode 5-6Simple Mode 5-3

1D Processor Tool 5-31D slice 7-9, 9-71d.delta_parameters E-402D Data

Data Reduction 7-23Display Modes 7-14Integration 7-27Loading 7-1Mesh Mode 7-14Panning 7-21Peak Grouping 7-25Phasing 7-10Plotting 7-30Stack Mode 7-14Surface Mode 7-14Zooming 7-21

2D Phasing Tool 7-102D Processor 7-32D Viewer 7-13

Overview Area 7-21Projection Area 7-22Slice Area 7-22window 7-17

2d.delta_parameters E-443D Data

Panning 9-18Zooming 9-18

3D Data Viewer 9-83D Slicer 9-123d.delta_parameters E-44

AAbs Intgrl 4-45accelerator keys 1-2, 2-5, 3-3Acquisition

Auto-Place E-34Experiment Section 10-26Macro 10-47Multiple Buffers 10-40

Parameters 4-30active window 2-3ADC E-48ADC_PIPELINE_DEPTH E-48AIX L-2All Overlays E-23Allow Author Login E-33Allow Connect E-36ALLOW_MONITOR E-48ALLOW_OWNED E-49Amplifier Power Settings 10-42Annotation 5-55, 7-27, E-23

Rotating 7-29Shifting 7-29

aqp_program E-64AQP3_VERSION E-49Arrayed Parameters 8-1, 10-48assignment

groups E-8residues E-8types E-8

AtomNumbers E-29Select Numbers E-29Sequence E-29

Attenuators 10-46Audio filter 10-25Author E-18Auto Console E-34Auto Directory Submit E-33Auto Level Tool E-34Auto Process 5-9Auto Reference 5-35AUTOGAIN_LOWER E-49autolock 4-19Automation 4-1, I-4

Advanced E-36Lock E-42

Console 4-38customizing 4-41E-Mail File E-33file 4-39Gradient Shim E-43Gradient Shim Allowed E-43multi-user 4-43Temp. Lock E-42, E-44

Index-ii Delta User’s Guide, v3.2

templates 4-40Automation Editor 4-1, 4-35, 4-39, 4-42, F-

1, F-9Automation Queue 4-1, 4-35, 4-36, 4-37Automation Queue Window 4-37automation templates F-1Automation Tool 4-34Auto-phasing 5-30Autosample Changer

slot 10-19autoshim 4-20autoshim status 4-19auxchestrc E-14Axial Units 5-33

Bbackup_spectrometer E-16Balloon Help E-18

Delay E-18Time E-19

Base_correct 5-14baseline correction 5-30BBUS_INTERFACE E-49Bell

Sound E-33Bias slider 7-19Black and White Icons E-33blink.cof E-67Border E-28Button Press Freq. E-19

CCalculations 10-36

Audio Filter Delays 10-37Pulse Angles 10-36Pulse Widths 10-36

Center E-28CHANGER E-49CHANGER_MAX_CHANGE_TIME E-

49CHANGER_TIMEOUT E-49CHANGER_VERSION E-49chemical shift reference 4-13COLLECTED_SOUND E-50Collection Mode 10-43color

background E-32

datazone E-32foreground E-32highlight E-32mode E-33PM Unselected Color E-32printer E-22selected E-32

comment E-23config_modem.sh E-64Configuration Editor 1-2Configuration Files E-17Confirm window 3-6Confirmation E-19CONNECT_DEVICES E-50Connected Objects 6-11Connection Tool 3-5, 6-11

Init E-36Console 4-38, E-3

Color E-34Coloring E-34Cut & Paste E-34History E-35Wrap E-35

Console Log File E-33console mode 4-7Contour E-24contour line

Check E-24limit E-24

Contour-line level button 7-19control_aqp2, control_aqp3 E-64convert E-8

-o switch E-8convert NMR Data E-8Copy References Tool 5-36copy_setup E-14, E-15COSY

Peak J Width E-35count E-67Coupling Constants 5-46CPU performance 3-1Cryogen

cryogen.log file E-66cryogen level 4-10cshrc E-14Current parameter value 10-10

Delta User’s Guide, v3.2 Index-iii

Cursor I-4Reference 5-34

cursor E-24operation 5-20pick 6-15, 9-16

Cursor Mode 5-20, E-28Cursor Tool 5-19, 5-20, 5-22, 5-36, 9-15,

E-28Open E-28

Cursor Tool Tab 5-20

DData E-19, E-24

uploading 4-5Data Color

Slot n Imaginary * E-32Slot n Real * E-32

Data DisplayContour Display 7-17Datadex Mode 7-15

Data Geometryoptions menu 6-13

Data Page 3-12data points 10-28, E-24Data Reduction 7-23, 9-18Data Set

Active 6-5Connected 6-11connecting 3-5Multiple 6-3Presentation Control 6-12

Data Slate 3-4, 6-13D 9-8Advanced Operations 6-15Connect All E-37Connect Features E-37Connect X E-37Expansion 6-17Horizontal View 6-3Plot Parameters E-37Plot Process List E-37Save Plot Parameters E-37Slicing 6-15Vertical View 6-3

Data Viewer 3-4Datadex Mode 7-15Date Format E-36

DC Balance 5-13dead_time 10-37Debugger I-3Deconvolve E-24

Sum E-24Unselected E-24

Decoupler Sequences D-2Decoupling 10-34, 10-35, 10-42, 10-46,

10-48, D-1Bilevel 1H D-2Proton D-1

Deleting Queue Items 4-23delta 3-1, E-1, E-3

experiments directory E-1instrument directory E-1library directory E-1p_files directory E-1process_lists directory E-1reports directory E-2templates directory E-1

Delta Configuration Files E-17Delta Console 3-1, 3-2

Accelerator keys 3-3Menu Bar 3-3User menu 3-3

Delta Console Preferences Tool E-17Delta Console window 2-4Delta Software Installation L-1Delta Upgrade Spectrometer D-1Delta.icon E-2, E-14delta_automation.auto 4-35delta_automation.auto_automation E-13delta_configure 3-9, 4-5, 4-25, E-1, E-14,

E-15, E-17.delta_configure_root E-15

delta_drop E-14delta_parameter_list E-14delta_product_key E-3, E-6, E-11delta_screen.rgb E-11Dependency Graph window 4-40Dept/Inept I-3dept_automation 4-42dept_filter 4-42dimension features 10-6ding.aifc E-12directory tool 3-10

Index-iv Delta User’s Guide, v3.2

domain X E-62Domains 7-4, 9-2, 10-27, 10-35

Active 7-4, 9-3dot files

auxchestrc E-14cshrc E-14delta_automation.auto E-13delta_configure 1-2, 3-2, E-17delta_configure_root E-15delta_parameter_list E-14delta_product_key E-3grosview E-14login E-15

Double Click Rate E-19download E-67Drag Delay E-19Draw

Backface E-24Blend E-24Dither E-25Double Side E-25Gradation E-25Smooth E-25Solid E-25Texture E-25

Eeclipse 1-1, E-60, E-65

/eclipse Configuration Files E-46/eclipse Program Files E-64/eclipse/probes E-60/eclipse/shapes E-63

Eclipse NMR spectrometer 1-1, 4-1directories E-1

Edit 4-40Edit Sample Window 4-40Editor E-18Enable E-28end domain E-62entropy functional 5-18eps files E-13etc/init.d E-68Ethernet traffic 4-4exceed_delta.kbf E-15, M-2Executable E-19exodus_delta.bin E-15Expansion 6-17

Experiment 4-1, 4-8, E-19, F-4Compiling 10-48Definition 10-1Error messages 10-48Header Section 4-26Instrument Section 4-29Loading 4-26, 10-2Macros 10-43Operators 10-7Parameters 10-10Phase Tables 10-38Pulse Section 4-31Section 4-40Selection 4-25Sequential Execution 4-42Syntax 10-7Total Time 10-38

Experiment files 4-26Experiment Tool 4-1, 4-24, 10-4

Hints E-37Extended Mode Icons 5-10

FFast Fourier Transform 5-18FFT 5-13, 5-18FG_CONTROLLABLE E-50FID 4-44, 5-2, 5-3

Audio E-33FIELD E-50File E-25

Name E-25File Manager 3-4, 3-15

Delete Dir Update E-38Delete Whole Dir E-37Require Ack Update E-38Require Acknowledge E-38Show Errors E-38Show Errors Update E-38Show Hidden Files E-38

files E-2./files/data E-2./files/foreign_data E-2

FILTER_LIMIT E-50fixup E-10Font conventions 1-1Foreign Data E-20Format Converters E-8

Delta User’s Guide, v3.2 Index-v

Freeze Slot E-28Frequency Offset 10-46

Ggamma.def E-46Gate Assignments 10-45Geom Border E-25Geom Tools E-35

Tracking E-35Geom Windows E-28Geometry

Hints E-27Negative Contour Grey E-23Persistent Mode E-27Rotation E-28

Geometry Page 3-13get_spectrometers E-15gif Files E-13Global E-20

Data E-20Executable E-21Experiment E-21Foreign Data E-21Instrument E-21Library E-21Process List E-21Report Output E-21Source E-21Template E-21

global.rgb E-11global_percival_operator_library.1 E-7gr_osview 2-8Gradient E-50Gradient Shimming 4-19Grid E-25grosview E-14Group 4-42

Section 4-40, F-3GSX_AUTOLOCK_TRANS E-50GSX_COMPAT E-50GUI 2-1, 2-2gx filename E-8gxscon.scn E-65gyromagnetic ratio 4-13

HHamming 5-13

handles 2-6Header Flags 4-26, 10-19

Adding 10-23Header Parameters 10-10, 10-22

Adding 10-23Header Section 10-17Help 3-5, 3-6HOLD_DELAY E-50html Files E-13hw_debug E-67

IiBase_Correct window 5-30IBM L-2icons E-2ident_sipp E-67IDLE_LOCK E-50Include Files

System 10-16User 10-16

input file filter 5-4input focus 2-3INST_TYPE E-51Instrument E-18, E-20Instrument Parameters 4-29, B-1

Adding 10-26Instrument Section 10-23integral E-25

2D 7-27normal E-25Precision E-25search width E-35Tails E-26Value E-26

Integrals 5-39Slope adjustment 5-48

Integration 5-36, 5-50Manual 5-47

Intel L-1Interactive E-29interrupt.cof E-67interrupt_test E-67IRIX L-1irr_code 10-34, 10-47, C-1, E-62Irradiation Codes C-1Irradiation Modulation 10-47

Index-vi Delta User’s Guide, v3.2

Jjdc E-5JEOL AutoTune probes K-1JEOL Delta Compiler, jdc E-5jeol.eps E-11

Kkermit-C E-15Keyboard commands 5-20Keystroke conventions 1-2

LLC-NMR

measurement tool 4-35Level Tool 5-59, 7-17

Pop E-35window 7-18, 7-19

LG_SHIMS E-51library E-20Line Editor I-4Line Hiding E-26Linux L-1list_header E-11local E-68local.rgb E-11lock

channel circuits 4-19control 4-10, 4-18signal level monitoring 4-20solvent 4-10

selection 4-12status 4-19

lock channel circuits 4-19Lock Level Meter 4-10, 4-17lock solvent 4-10LOCK_TIMEOUT E-51login 2-1, E-15login.icon E-2, E-15Logout 2-9LOW_HE E-51LOW_N2 E-51

Mmachine

.alarms E-65

.authorization E-66

.connect E-59

.defaults E-59

.idle_lock E-59

.log E-66

.old E-66

.post_exp E-60

.pre_exp E-59machine.config 4-5, E-46, E-48machine.info 4-3, E-56machine.lg_shims E-56machine.mx_shims E-56machine.poll_speeds E-56MACHINE_LOG E-51MachinePhase 5-30macro

redefining 5-13Macros 10-43

Acquisition 10-47magnetic field strength 4-9, 4-13make_copy E-66Max Peaks Allowed E-26MAX_FG_PULSE E-51MAX_FILTER_POINTS E-52MAX_POINTS E-52MAX_PULSE E-52MAX_SCANS E-52Maximum Entropy 5-18Menu 3-3method

buttons 4-36file 4-35section 4-40, F-2

MINIMUM_LOCK_STRENGTH E-52Miscellaneous Page 3-14mod return parameter 4-44module_config 10-41, 10-47Molecule

Borders E-29Titles E-29Windows E-29

Mouse Cursor Toolintegration operations 5-46

MR spectra 5-18multi_file Option 10-48Multiple Buffer Acquisition 10-40

NnD Processor

Tool 7-1

Delta User’s Guide, v3.2 Index-vii

nD Processor Tool 7-1Negative Levels E-31

On E-27NMR

data 3-1NMR processing 1-1No Auto Contour E-29No Zooming E-29node 4-2node names 4-2, 4-7Noise Modulation 10-46

Gating 10-42NOT_COLLECTED_SOUND E-52nsend_message E-6

Oobs1, obs2, irr1, irr2, tri, qua E-52offset 4-20Open Experiment window 4-25Open File Tool 5-4, 5-6Open Shim File window 4-16OPERATION_PROTECT E-52Operator Cache E-34Options 6-13OSC_1H E-52Overlay Offset X E-29Overlay Offset Y E-30Overview 7-21, E-30

Pp Files E-5, E-16page size E-22Panning 7-21, 9-18parameter 3-5, 4-43

location E-22parameters 3-5Password E-18paste 3-5PC X-Servers M-2peak E-26

Above E-26Color n * E-32integral E-22, E-26Threshold On E-30

Peak Deconvolution 5-51Peak Display 5-45Peak Grouping 7-25

peak intensities 8-7Peak mode

deleting peaks 5-37Peak Pick 5-41, 7-23, 9-18Peak Picking 5-36

Automatic 5-39peak position 5-35performance monitor 2-8Personal Page 3-7, E-18Perspective E-30PGX-300 10-44phase 4-20

manual 5-27phase correction 5-28Phase Sets

Addition 10-39Concatenation 10-39

Phase Tables 10-38phase_automation 4-42Phases

90 degree 10-40Phasing

Pivot Point 5-29phasing

2D Data 7-10ping 4-7PiP

Font Factor E-30PiP mode 5-25plot

All Text E-30Plot Border E-23Plot Dialog E-23Plot Options E-22Plot Tool 5-68Plot Transparent E-26Plotting 7-30PM

Center Y-Scale E-38Font Size E-39Plot Process List E-39Template E-20

pmt files E-13pmt_presentation mgr E-13Positive Levels E-27, E-31PP 5-29

Index-viii Delta User’s Guide, v3.2

PPM 5-14pps _ presentation mgr E-13Preferences Tool 3-1, 3-7, 3-10, 4-5

changing parameters 3-10search window 3-10

Prescans 10-29Presentation F-4Presentation Manager 3-4

Operator G-1Presentation statement F-7Presentation window 4-40Preserve Position E-35PRESERVE_DIALS E-53Preset button 7-19Prettify 5-25print

JEOL logo E-22Printer E-22

Orientation E-22Paper Size E-22Tessellate E-22

probe E-62Probe Attributes 10-33Probe Codes 10-32probe file 10-32Probe Tuning K-3

Values 10-35Probe Variables 10-36probe_coarse E-63PROBE_DELAY E-53probe_match E-63probe_tune E-62Process 1D

Macro Definition E-40Macro Order E-40Plot Parameters E-40Plot Process List E-40Save Auto Apply E-40Save FID E-41Save Macro Def E-41Save Macros E-41Save Plot Param E-41Save Simple Mode E-41Save Timing E-41Save Tools E-41Show FID E-40

Show Macros E-40Show Timing E-41Show Tools E-41Simple Mode E-41View Precision E-40

process command line 4-28Process FID E-30Process nD

Plot Process List E-42Process_Global 4-29Process_Interactive 4-29Process_Interactive_Global 4-29Process_Interactive_Local 4-29Process_Local 4-29Process_ndimensional 4-29processing history 3-5Processing List 5-7

Display functions 5-26PreTransform 5-14Transform functions 5-17Window functions 5-17

processing list 10-18, E-20, E-373D 9-3

pulcon.pul E-66pull E-15pulse

90’s 10-3390˚ pulses E-62

Pulse Parameters 10-13Pulse Programs 10-44Pulse Section 10-29pulse viewer 4-32PULSER_TICK E-53

Qqueue 4-8, E-57

.log E-66

.old E-67Queue Control States 4-21Queue Modes 4-21queue.hours E-57queue.priorities 4-21, E-58QUEUE_LOG E-53

RReal Time 4-8, 4-44Real Time monitor display 4-8

Delta User’s Guide, v3.2 Index-ix

receiver gain 10-24Reference 5-35, I-3Reference Command 5-35reference registers 5-35Reference Tool 5-34reference value 5-35Referencing 5-34, 7-23Region Manipulation E-30Region mode 5-24regions E-26Relaxation Data 8-1

Calculation 8-3Collection 8-1Processing 8-2

relaxation delay 4-44, 10-30Relaxation Times 8-3Report Output E-20restore_spectrometer E-16Resulting File window 6-11RF filters 4-20RF Phase 10-46RF_SHAPER E-53

Ssample 4-7, 4-10, F-1

changer 4-10, 4-23loading 4-1, 4-7, 4-10spinning 4-10, 4-11state 4-10temperature control 4-12

Sample Control Tool 4-9, 4-43Gradient Shim E-39Verify E-39

sample ID 4-21sample name 4-21SAMPLE statement F-1Sample Status 4-36SAMPLE_DELAY E-53SAMPLE_SOUND E-53Save Color & Font E-35Save Data File window 5-67Save Shim File window 4-16Saving Processed Data 5-6sawth 4-1

window 4-43Sawtooth 4-43

Lock Signal Display 4-43

SAWTOOTH_SHIFT E-53SAWTOOTH_TRIM E-54Scale Solvent E-27scans 10-28Send_data_to_finger 4-29send_message E-5sequence

marker E-27Set process window 4-27SGI L-1Shadow Dimensions E-27shim control 4-10Shim Files 4-15Shim Tool 4-13

Controls 4-14Nomenclature 4-14

shim values 4-20SHIM_KNOB BOX E-54shims 4-10

loading from data files 4-10spinning and nonspinning 4-14

Show Deconvolution E-36Show Peak Count E-36Show Tools 5-3Silicon Graphics user interface 2-1Simple Mode E-19

Processor Buttons 5-79Single Buffering E-34Single Exponential 5-17Site E-18slice

slicing 6-15Solaris L-2solvent 10-24solvent.def 4-19, E-58SOUND_DURATION E-54Source E-20Spectral Offset 10-27Spectral Widths 10-28Spectrometer 4-1

connection 3-5Load E-34monitor E-34monitoring 4-6selection 4-2unlinking 4-7

Index-x Delta User’s Guide, v3.2

Spectrometer Control Tool 4-1, 4-2, 4-7,10-2

Double-Click E-39functions 4-3Gain 4-19Locking 4-18Menus 4-9queue menu 4-21Selection 4-2Solvents 4-18Tools 4-7

spectrum 5-18Spin Lock Pulses 10-34SPIN_GAS_SOURCE E-54spin_lock_90 E-62spin_lock_attn E-62SPIN_SLOP E-54SPIN_TIMEOUT E-54spinning_delta#.RGB info E-12Spread Sheet I-5Spreadsheet 3-5Spreadsheet Tool 5-64, 7-30standard files 4-26Standard Include Files A-1Start slider 7-18Startup

Default 5-3Startup Console E-18Statements

Align 10-14Assignment 10-8Collect 10-43Conditional 10-15Define 10-12Loop control 10-15Macro 10-14

Statistics E-27std_2d_acquisition A-1std_3d_acquistion A-2std_acquisition A-5std_header 10-17, A-4std_include 10-17std_instrument A-5std_pulse A-5Stereo E-30STRICT_SOLVENT E-54

Sun L-2Supervisor Alert E-43SUPPRESS_FW_WARNINGS E-54Sweep Widths 10-28Sweep/Offset Adjust E-36swept lock signal display 4-8SYNC0_BUS_LINE E-54system Delta directories E-1System Usage 2-8

TT1 Analysis I-3T1 Analysis Tool 8-1TEMP_HOLD E-54temp_limit_hi E-62temp_limit_lo E-62TEMP_SLOP E-55TEMP_TIMEOUT E-55Temperature 10-25

control 10-25Limits 10-34Parameters 10-25

template E-20Template File Format G-1terminal console program H-1Terminal shell 2-8test_lights E-68test_serial_fiber E-68Time-shared Homonuclear Decoupling 10-

42Toggle Slot E-31Tool Bar 3-3Tool Bar Icons 3-3Tool Icons

1D Processor I-63D Plotter I-6Automation I-3, I-4Automation Editor I-4Autoqueue I-3Calculator I-3Chart I-4Connect I-4Connection I-5Console manager I-2Cursor I-4Data slate I-3Debugger I-3

Delta User’s Guide, v3.2 Index-xi

Delta console I-2Dept/Inept I-3Experiment tool I-2Export I-2File Math I-2Geometry tool I-2Get directory I-1Import I-2Interactive base correction I-2Level I-4Line Editor I-4nD Processor I-7Parameter Editor I-4Parameter tool I-1Parameter Viewer I-6Peak List I-6Phase 2D I-1Pick tool I-1Preferences I-5Presentation Manager I-1Presentation Manager template I-1Process I-7Reference I-3Signal/Noise I-5Spectrometer I-5Spread Sheet I-5T1 Analysis I-3Template I-6Transfer Integral I-5View Control I-5Widget Editor I-6Window Phaser I-6

Toolchest 2-6, 3-1Tools

Experiment 10-5Tools page E-36total_time 10-30Track Position E-31Transform Function 5-17Transparent E-31Transparent X Ruler E-31Transparent Y Ruler E-31Transparent Z Ruler E-31TSC_AVAILABLE E-54TSC_TIMEOUT E-55

UUnix J-1Unix Commands J-1UNIX Shell 2-9Unlink 4-7update_spectrometer E-16Upgrading an Acquisition System

AIX L-8Linux L-7SGI L-5Solaris L-7

Upgrading the Delta SoftwareAIX L-7Linux L-6SGI L-3Solaris L-6

upload E-7UPLOAD_EXPIRE E-55User Account E-1, E-14USER Account Setup L-8USER Setup E-14User Shims 4-16usr/delta

/usr/delta/eclipse E-16/usr/delta/eclipse/probes E-16/usr/delta/source E-16usr/delta/eclipse/dist E-16

usr/delta/global E-6, E-7, E-11, E-13Files E-3usr/delta/global/automation E-13usr/delta/global/experiments E-13usr/delta/global/help E-13usr/delta/global/process_lists E-13usr/delta/global/templates E-13

usr/delta/global Directories E-13usr/delta/global/automation E-13usr/delta/setup E-14usr/eclipse E-66usr/eclipse/testprog E-67

Vvariable temperature 4-10Vector View

Auto Off E-39Processing E-39

verify E-6VI Commands J-2

Index-xii Delta User’s Guide, v3.2

View Control I-5View Tool 4-1, 4-8, 4-44View Vector 4-44virtual geometry 3-2VTEMP E-56

Wwidgets 3-1Window

Full screen 2-6Iconifying 2-5Menu Button 2-4Moving 2-6Resizing 2-6Structure 2-3

XX Display Manager M-1X ruler E-31X Windows Emulation M-1x_90_width 10-30xxxx

.dials E-63

.limits E-63

.probe E-60, E-62

.shims E-63

.shims.0 E-63

YY ruler E-31

ZZ ruler E-31Zerofill 5-15Zoom mode 5-23Zooming 9-18

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