nuts n mr u tility t ransform s oftware acorn nmr, inc. livermore, ca

NUTS

NMR Utility Transform Software

Acorn NMR, Inc.Livermore, CA

Menus – where to find thingsProgram basics

Base level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data

Getting HelpManualHelp files

Opening data filesData and import directories“Tailer”

ProcessingBaseline correction of FIDExponential multiplicationFTPhasingBaseline Correction

Integration Peak Picking

PrintingCopying Structures on screen

MO subroutineCustomizing NUTS

nuts.ini fileAutomation

Command linksMacros

MenusFile – import, open, save files; print, run macro

Edit – Un-Do, copy (Copy options discussed later)

Open GASave SA

Print PL

Import IM

Run Macro RU

UnDo ^Z

Copy Enhanced Metafile Alt-Shift-E

Menus, cont.View

Spectral Parameters

Spectral Parameters – acquisition parameters

Show Integrals ^I

Toggle on/off display of integrals

Show All ^F

Display full spectrum Start Zoom ZO

Enter Zoom expansion subroutineShow Peak Labels ^P

Toggle on/off display of peak labels

Show Zoom ^E

Display expanded region

Spectral Parameters

Menus, cont.Process

Conditions – linebroadening, Minimum height, phase parametersWindow functionsFTPhaseBaseline correctionEnter integration routinePeak pick

Phasing >

Baseline Correct BC

Quick Baseline QP

Automatic Integrate AIPeak Pick PPIntegrate Display ID

Processing Parameters

Menus – where to find thingsProgram basics

Base level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data




Integration Peak Picking

PrintingCopying Structures on screen

MO subroutineCustomizing NUTS

nuts.ini fileAutomation

Command linksMacros

Program Basics

Scale data with scroll bar, < and >, Page Up/Down

Base level

2-letter keyboard commands, same as menu commandsDoes not require <ENTER> to execute commands

Press left mouse button to display frequency at bottom of screen

To measure frequency differences (coupling constants):Press and hold left mouse buttonPlace vertical cursor on one peakClick right mouse button (do not release left mouse button)Move cursor to another peakFrequency difference displayed at bottom of screen

Subroutines (Zoom, Integration, etc.)Watch status barSingle-letter keyboard commandsMouse function varies with subroutineExit with <ENTER> keyDon’t use buttons!

Zoom subroutineEnter Zoom by:

1. View/Zoom menu2. ZO keyboard command, or3. Double-click left mouse button

• <ENTER> to exit Zoom• Ctrl-F for full display, Ctrl-E for expanded display• In Zoom, select zoom region by pressing and holding left mouse button, and wipe across chosen region• Avoid single-click of left mouse button (this selects a region consisting of a single data point)• Right mouse button toggles between full and expanded displays

Program basicsBase level and subroutinesMouse functionsKeyboard commandsZoom expansion routineScaling data




IntegrationPeak PickingPrintingCopying

Structures on screenMO subroutine

Customizing NUTS nuts.ini file

AutomationCommand linksMacros

Manual – 1st 170 pages covers 1D processing http://www.acornnmr.com/Downloads/NUTSmanual.pdfContains command list, table of contents

Help FileTable of ContentsKeyword indexFull text search

Web sitehttp://www.acornnmr.com/NutsHelp

Help!

Where are my files?Working “data” directory – Open (GA) and Save (SA) commands“Import” directory – where NUTS looks for foreign files (IM)

These paths are defined in nuts.ini, but change dynamically as files are opened or saved

WP (Which Path) command – where am I?

Import data with IM command

Save processed data with SA command

What is saved in my file?Data is saved as you see it on the screenIntegrals, Peak list, etc, saved in file “tailer”

Auto Tailer Read option under the File menu – controls whether or not integrals, etc, are read when a file is opened; can be set in nuts.ini file

Baseline correct the FID – BCto prevent “center glitch”

DC offset between real and imaginary FIDs

Offset creates glitch BC removes glitch

Exponential MultiplicationSet linebroadening parameter (LB) and execute with EMImproves signal-to-noise at expense of peak broadening

FT

Phasing with NUTSStart with QP – quick automatic phasingTouch up phasing with one of the manual, mouse-driven phase routines

Manual phasing with mouse Left and right mouse buttons apply zero-order and 1st- order correction

PH – Do this on full spectrumSet pivot point – place cursor and type P

Zero-order correction with left buttonAdjust peak at pivot point

First-order correction with right button to phase the rest of the spectrum

Exit subroutine with <ENTER> key

PE – Phase Expanded, for more close-up viewdefine 2 regions, phase each using expanded displaySwitch between regions with 2 mouse buttons

To define the 2 regions, use Zoom:

select 1st region, type 1 select 2nd region and type 2

Exit Zoom and enter PE routine

Phase Region 1 with Left button Phase Region 2 with Right button

Exit subroutine with <ENTER> keyPhase correction is applied to entire spectrum

Baseline correction of the spectrum

Distortion can be combination of DC offset – removed by BCLinear tilt – removed by BCHigher order roll – polynomial

Best method of correction is dependent on characteristics of each spectrum

Poor baseline may be most apparent when viewing the integral – if it isn’t flat, the baseline isn’t at zero.

QB (Quick polynomial Baseline correction) works in most cases, especially if peaks are sharp and signal-to-noise is good.

More baseline correction features are available; see Help

Automatic Integration – AI

Integrates all peaks above Minimum Height (MH) threshold

Sets smallest integral to 1.0

If full spectrum is displayed, AI clears previous integrals before integrating

If expanded region is displayed, AI appends integrals to a growing list, allowing successive selected regions to be integrated to create a complete integral list. Scaling is not re-set for successive regions.

Works best for spectrum with well-resolved peaks and no impurities

Manual integration

ID subroutine, exit with <ENTER>

Scaling the integral vs. scaling the spectrum

Correct the baseline, not the integral!

Define start and stop points for each sub-integral by left mouse clicks

Assign a convenient value to one of the sub-integrals with V key

The scaling factor remains until explicitly changed, regardless of scaling.

Whether created automatically or manually:

Integrals remain after exiting ID subroutineToggle on/off display of integrals with Ctrl-I (or Tab key)

Integral regions remain defined when you open a new data file

Integral regions are saved with the data

User chooses whether or not integrals are read in when the file is opened at later date






Structures on screenMO subroutine Customizing NUTS nuts.ini file


Peak Picking - PP

Set threshold (minimum height) with cursor and M key or type MH

Each PP operation replaces previous peak list

Peak list is automatically copied to the clipboard

Peaks outside current display region are not selected

Toggle on/off peak labels with Ctrl-P or from View menu

Labels remain when you open a new data file

Peak list is saved with the data

User chooses whether or not peak labels are read in when the file is opened at later date





Integration Peak PickingPrintingCopying




Printing

PL

From inside some subroutines, command is just P

WYSIWYG – What You See Is What You Get

Print setup dialog box appears only the first time you print





Integration Peak Picking PrintingCopying




Copying to Word or PowerPoint

Options found in the Edit menuBitmap“Metafile” – vector drawing; usually better quality

For historical reasons, there are several variations of Metafiles

Enhanced Metafile works best in most cases

Best choice of parameters depends on starting and final size of image

Details can be found in Help file and manual

7 6 5 4 3 2 1 0 PPM

Enhanced metafile – probably fine for most needs

If you shrink the figure, text (axis numbers) may get too small to read

Copied as bitmap and expandedScreen resolution is fuzzy

7 6 5 4 3 2 1 0 PPM

Enhanced metafile, copied then expanded Note that numbers on axis are sharp, not fuzzy

When expanded, observe distortion caused by an integer round-off problem by target application

Integer round-off can be minimized by maximizing size of NUTS screen

7 6 5 4 3 2 1 0 PPM

Round-off problem can be avoidedCopied to a file as enhanced metafile with “printer device context, then inserted and expandedResult is very high resolution

7 6 5 4 3 2 1 0 PPM

Enhanced metafile created with macroSet colors to black, increased font sizeWhen size is reduced, numbers still readable





Integration Peak Picking Printing Copying




Putting structures on screen - MetaObjects (MO) subroutine

Paste structure from clipboard or import Windows Metafile (.wmf)

If imported from a file, a “pointer” to that file will be saved when the data file is saved, so can be recalled later

Can create, move, re-size multiple objects

Can also be used to create inset plots, but Inset Plot routine (IS) usually gives better results

Nuts.ini – text file read by NUTS when it is launched

Contains user preferences for:Import and data directoriesAutomatically read “tailer” data when opening a fileDefault LB valueAutomatic peak pick when MH is set with cursorUn-Do on/offFonts – integral, peak labelDefine zoom regions (eg, 0-10 ppm for plots)Pre-defined command links and macrosColorsMargins

Includes description of each parameter and how to set it

Automation

Command “links” – frequently used string of commands LI – display link definitions (set by nuts.ini)A# (where # = 1, 2, …) executes the corresponding Link

Example for routine processingbc em ft qp

Macros – text files containing NUTS commandsMore flexible and powerful than Links

NUTSMACRO auto-1D batch processing;FT, auto-phase and baseline correctset lb 0.3; set zoom region #5 to 10->0 ppm, for plottingset zoom_region 5 10 0

;set zoom region #6 for aromaticsset zoom_region 6 9 6

;set zoom_region #7 to downfield regionset zoom_region 7 15 10

; set zoom region #0 to TMSset zoom_region 0 .3 -.3

loop 27 45pf idc^m isc^m ^f af mfff bc ft ap it em ft psz0 ê sz z5

; initialize size & position for first IS inset2fis xsize .55,is ysize .5,is xpos 0,is ypos 0,2n,; display aromatics full scale and create insetz6 ê mf isa^m

; initialize size & position for downfiled IS inset2fis xsize .25,is ysize .1,is xpos 1,is ypos 0,2n,

; increase vertical scale 3x and create insetset ac 3acz7 ê isa^m

; display 10->0, adjust scale, PP and enter integrationz5 êset ac 0.1ac

; set MH for peak pickingset mh 10pp

; auto-integrateset mh 1aian

;save processed filesaend

8 6 4 2 PPM

7.8

25

7.7

60

4.1

45

4.1

33

3.9

81

3.3

15

2.5

10

2.5

06

2.5

01

2.4

96

1.1

45

1.1

27

1.1

09

0.0

00

0.91

4.12

2.00 2.06 2.00

1.03

6.04

4.00

8.5 8.0 7.5 7.0 6.5 PPM

14.5 14.0 13.5 13.0 12.5 12.0 11.5 11.0 PPM

Advanced Features

1D:Inset plotsText annotationInteractive baseline correctionLine-fit (deconvolution)Spectrum simulation from chemical shifts and couplingsLinear predictionDual displayAdd/subtractStacked plotsMath

2D processing and display

The End

nuts n mr u tility t ransform s oftware acorn nmr, inc. livermore, ca

Documents

peakclick right mouse

left mouse buttonmove

thingsprogram basicsbase

screensubroutines zoom

zoom ctrlf

page updownbase level

chosen region

command list