crystalmaker tutorial

Interactive Visualization forCrystal & MolecularStructures

CrystalMaker®

CrystalMaker

8.7for Mac OS X

CrystalMaker

2.7for Windows

Tutorial

© 2012 CrystalMaker software Ltd. All rights reserved.

An authorized user of a valid copy of CrystalMaker may reproduce this guide for the purpose of learning how to use the software. No part of this publication may be reproduced or transmitted for commercial purposes, such as selling copies or for providing paid-for support services, without the prior written consent of the copyright holder, CrystalMaker Software Ltd.

While the authors have tried to ensure that all information in this guide is accurate, CrystalMaker Software Ltd cannot be held responsible for any errors. In particular, because CrystalMaker Software Ltd frequently releases new versions and software updates, images shown in this guide may be slightly different to what you might see on your screen.

CrystalMaker Software Ltd make no representations, express or implied, with respect to this guide or the software it describes, including without limitations, any implied warranties of merchantability or fitness for a particular purpose, all of which are expressly disclaimed.

Mac is a trademark of Apple Inc., registered in the U.S.A. and other countries. Microsoft, Windows and the Windows logo are trademarks, or registered trademarks of Microsoft Corporation. CrystalMaker, CrystalDiffract and SingleCrystal are trademarks or registered trademarks of CrystalMaker Software Ltd.

Special thanks to Charles Prewitt, John Geleynse, Liang Hoe, Robert Kehrer, Martin Dove, Tim Holland, Joel Miller and Yoshitaka Matsushita

Last updated: 20 November 2012

3

Contents

Preface Tutorial Overview ..............................................................................4

Section A Building an Inorganic Structure ........................................................5 Structural Data ....................................................................................5 Entering Crystal Data .........................................................................6 Changing Atom Colours & Radii .......................................................9 Defining Bonds ..................................................................................10 Adding Notes ....................................................................................11 Getting Help .....................................................................................12 Saving a Crystal File ..........................................................................12

Section B Displaying a Crystal .........................................................................13 Opening a CrystalMaker File ............................................................13 Resize The Plot ..................................................................................13 Changing the Plot Range ..................................................................14 Changing The Background Colour ....................................................15 Rotating The Structure ......................................................................16 Specifying A Rotation Angle .............................................................17 Defining a View Direction.................................................................18 Changing the Crystal Model .............................................................19 Rendering Modes ..............................................................................20 Atom Styles .......................................................................................21 Bond Styles ........................................................................................22 Polyhedral Styles ................................................................................23 Site Browser .......................................................................................24

Section C Probing the Crystal ..........................................................................25 Tools Palette ......................................................................................25 Zooming an Area of Interest .............................................................26 Atom Info ..........................................................................................26 Measuring Distances and Angles .......................................................27 Working with Lattice Planes .............................................................28 Angles between Planes & Vectors ......................................................29 Hiding Atoms ....................................................................................30 Local Coordination Environments ....................................................31 Local Embellishments .......................................................................32 Generating a Distances & Angles File ...............................................33 Publishing a Web Page ......................................................................34 Summary ...........................................................................................35 Dynamic Visualization ......................................................................35 Learning Resources ............................................................................35

4

Preface

Tutorial Overview

CrystalMaker is a powerful program, but this tutorial is designed to quickly familiarize yourself with its key features. This tutorial is divided into three consecutive sections, designed to illustrate different aspects of CrystalMaker’s capabilities. We recommend that you follow all the steps (indicated by the numbered boxes, “ 1 ” )in order to build up your understanding.

In the first section, we shall build a crystal structure from scratch, using its spacegroup symbol, cell parameters and asymmetric unit. We then generate bonding and display one unit cell.

In the second section we expand the plot range, locate “missing bonds” and use explore different rendering modes and model types.

In the final section we use screen tools to measure the structure, display coordination clusters and export bond/angle data to a text file. Finally, we bring graphics and data together, by publishing a web page.

5

ABuilding an Inorganic Structure

CrystalMaker lets you build any kind of crystal or structure, with automatic symmetry-generation, bonding and polyhedra.In this section, we shall make a crystal structure model of the oxide mineral ‘spinel’ (MgAl2O4). We’ll start by defining the atomic positions, then proceed to edit colours, atomic radii, define bonds and polyhedra. We will use the resulting model for the rest of the tutorial.

Structural DataBuilding a crystal doesn’t have to be as painful as it might seem. This is because CrystalMaker can use any symmetry (including lattice translations) to build a complete unit cell from a much smaller, “asymmetric unit”—so you won’t generally need to type in the coordinates of every single atom! To display more extensive structures, CrystalMaker can tile multiple unit cells.

In this tutorial, we’ll build a structural model of spinel, MgAl2O4, an important oxide mineral. Here are the essential data we’ll need:

Crystal system: Cubic Spacegroup: F d 3 m (origin choice 2) Unit cell dimensions: a = 8.08 Å

Fractional coordinates of atoms in the asymmetric unit:

element x y z

Mg 0.125 0.125 0.125

Al 0.500 0.500 0.500

O 0.262 0.262 0.262

We’ll start by entering these data into the program, using the special editor window designed for crystals.

Structural data for spinel

Section A Building an Inorganic Structure 6

Entering Crystal Data1 Choose the File > New Crystal command.

2 The Edit Crystal window appears as a sheet (Mac) or dialog (Windows):

If the Spacegroup field isn’t already highlighted, press the tab key to highlight it.

3 Type the following characters into the Spacegroup field:

F d 3 m [origin 2]

(use spaces between the characters). If you make a mistake, CrystalMaker will warn you.

Where’s the Origin? Some spacegroups (such as this one) are slightly ambiguous, with more than one possible origin: perhaps at a centre of symmetry, or on a rotational element. For these space-groups, we need to explicitly specify the “origin setting” we’re using, so that our atomic coordinates are correctly positioned relative to the symmetry elements. This explains why we’ve added “[origin 2]” here.

If you’ve entered the spacegroup symbol correctly, all but one of the lattice parameter fields will vanish! CrystalMaker has recognized that your spacegroup symbol corresponds to a cubic crystal and that only the a unit cell parameter is required (for the cubic system, a = b = c; α = β = γ = 90°).

4 Press the tab key on your keyboard to move to the a field and type: 8.08. The editor window should resemble the following:

Unit cell entry for a cubic crystal. Note that only the

‘a’ cell parameter field is required: the unit cell shape is

constrained by symmetry

The Edit Crystal window

What’s a Lattice? If you are unfamiliar with the concept of lattices and unit cells, please refer to the Basic Crystallog-raphy appendix, in the CrystalMaker User’s Guide.

Crystallographic Units: Remember to use Ång-strøm (Å) units for unit cell dimensions. 1 Å = 10-10 m = 0.1 nm.


5 We shall now add three sites in the crystal’s asymmetric unit. Note that CrystalMaker requires the following information for each site:

• A unique site label. (Maximum of six characters, which must not include any spaces).

• One or more chemical element(s) and fractional occupancy values. (CrystalMaker uses element symbols to decide the atomic radius and the colour of an atom plotted for a particular site; element symbols can be one or two alphabetical characters.)

• Fractional coordinates, xyz for the site. These can be entered as fractions (“1/2”) or as decimals (“0.5”).

Click the Add button, or press the return key on your keyboard, to begin the process of defining a new site.

6 An entry appears in the list, with a default label, coordinates and site occupancy. We’ll need to edit these settings…

7 The site label should be highlighted; if not, click on it so that a focus ring appears around the site label and the old label is highlighted. Type a new label (up to six characters with no spaces)—we’ll choose: Al(1). Then press the tab key to move to the next editable field.

8 We’ll assume that this structure is ordered, so we only need to enter a single site occupancy value. Type “Al 1.0” in the site occupancy field.

9 Enter values of “0.5” in the “x”, “y”, and “z” fields, pressing the tab key to move between fields. Your editor window should now look like this:

10 Press the return key to finish editing this site.

11 You can now proceed to enter site data for the “Mg” and “O” sites, as given in the table at the beginning of this tour. Remember to click the Add button to create a new list entry or, to delete an entry, select that row and click the Remove button.

Defining our first site


12 When you have finished entering the crystal data, check that your editor window resembles the one illustrated below:

13 Click the OK button in the bottom right-hand corner of the Edit Crystal sheet or dialog.

14 The Edit Crystal window vanishes and a status window may appear.

CrystalMaker will now generate all atoms in the crystal, using the data you have supplied, indicating its progress in the status window. Once these steps are completed, a group of atoms inside a cube-shaped frame (the unit cell) is displayed in the Graphics window.

Complete structural data entry for spinel


Changing Atom Colours & RadiiIf you enter an element symbol that Crystal Maker recognises, the program will automatically assign colours and radii to all atoms with that symbol.

Customizing Elements: The elements that CrystalMaker recognizes are listed—with their col-ours and radii—in the Element Editor window (Edit > Elements). Experienced users can use this to switch between different preset Element tables (e.g., Van der Waals, Ionic, Covalent radii) or to define a new, custom element table. There is also a popup menu button in the window toolbar that lets you switch between the different tables.

If you wish to include other atom types in your crystal, or would like to override CrystalMaker’s default settings, you can explicitly define atom colours and radii—for the current structure—using the Site Browser, which can usually be found in the Graphics window’s Sidebar.

1 If the Site Browser isn’t visible, use the Window > Show Sidebar command to show the Sidebar. If for some reason the Site Browser still isn’t visible, choose the Window > Sidebar > Site Browser command.

2 We’ll edit the atom colours. The Colour column of the Site Browser contains buttons which allow us to change colours for individual sites, or for particular elements (i.e., one or more sites).

3 Click one of the coloured buttons and choose a new colour using the colour picker.

4 We’ll now edit the atomic radii, so we need to look at the radius column, which is labelled “r [Å]” to emphasize that radii are measured here in Ångstrøm units.

Click on the radius value for “Mg” so that it appears highlighted.

5 Enter a new value, say 1.0, and press return. The structure is replotted with larger Mg atoms.

Part of the Site Browser, showing atom types, colours

and atomic radii


Defining BondsWe can ask CrystalMaker to search for, and generate, bonds and polyhedra automatically. One way of doing this is to specify bonds by entering atom symbols and maximum bond lengths in the Edit Bonding window.

1 Choose the Edit > Bonding command. The Edit Bonding window appears.

2 Click the Add button to create a new, default bond specification.

3 We require Al–O bonds, so choose Al from the From popup menu, and O from the To popup menu.

We could type in minimum and maximum bond lengths for Al–O bonds, but instead we’ll ask CrystalMaker to choose sensible values, based on existing atom data built into the program.

Note that the maximum bond distance should be displayed in the Bmax field. CrystalMaker automatically calculates maximum bond distances as 1.15 × (rA + rB) where rA and rB are the radii of the “from” and “to” atoms.

4 Just to check that the bond range is sufficiently-large, click the Info checkbox, on the right-hand side of the bond specification row.

CrystalMaker summarizes the range of coordination environments encompassed by this bond specification, both for Al (6-fold coordinated by O) and for O (3-fold coordinated by Al). This summary will be useful when you need to refine bond specifications for new structures: you can experiment with min/max bond distances without having to constantly replot your structure.

5 Repeat steps 2–4, but requesting Mg–O bonds. When you have finished, the window should resemble the one shown below:

6 Click the OK button to replot your structure with bonds. Your structure should now resemble the one shown in the next section.

Missing Bonds? Notice that for this, single-cell view, not all atoms appear to be fully bonded. The “missing bonds” are to atoms that lie outside the current plot range, and which are therefore hid-den. We shall investigate ways of fixing this in Section B!

The Edit Bonding window, showing Al–O and Mg–O

bond specifications


Adding NotesYou can use the Notes pane in the Graphics window to store information about the structure. You can use the contextual menu in this pane to set colours, font sizes and other text attributes.

1 If the Notes pane is not visible, use the Window > Sidebar > Notes command to display it. (Alternatively, you could click the Notes button in the window toolbar.)

2 Click inside the Notes pane so that the insertion point becomes visible.

3 Try typing some text into the pane.

4 Use the Edit > Select All command to select all of the text.

5 Change the font. If you are using a Mac, you can use the Font Panel (Edit > Font > Show Fonts); Windows users will need to right-click to display a contextual menu and choose the Font command.

6 Select part of your text, then change its size, style and colour, using the contextual menu.

A Graphics window showing one unit cell of the spinel

structure. Notice the Sidebar, with formatted text in the Notes pane on lower right


Getting HelpCrystalMaker includes a highly comprehensive and searchable online help system. This can be accessed:

• Using the CrystalMaker Help command on the Help menu.

• Using the CrystalMaker Help command in a contextual menu.

• By clicking a Help button (“?” icon) in certain windows.

• By pressing F1 (Windows)On the Mac, help topics are displayed in the standard Help Viewer application and you can search for additional topics by typing keywords or phrases in that application’s Search field.

The Windows version of CrystalMaker uses a similar help viewer, which appears as a floating “palette” window.

Tooltips are available for buttons in the Tools palette and some window controls.

Saving a Crystal FileBefore we do anything else, we ought to save what we’ve done.

1 From the File menu, choose the Save command. Note that because this is a new crystal which hasn’t previously been saved, you’ll be presented with a standard file navigation dialog.

2 Select a suitable destination folder, and enter “Spinel Tutorial Crystal” for the filename. CrystalMaker will now create a binary file containing full details of the crystal structure, plus whatever text you have entered into the Notes pane.

Congratulations! You’ve successfully created and saved a CrystalMaker document. You might want to take a break now. You can choose the CrystalMaker > Quit command (Mac) or the File > Exit command (Windows).

CrystalMaker binary file icon

13

BDisplaying a Crystal

CrystalMaker lets you display as much of a crystal lattice as you require, using a range of model types.In the first section, we built a spinel crystal from scratch, and then saved it as a CrystalMaker binary file. We’ll use this file in the present tour, to investigate different crystal models, and to experiment with manipulating the structure on screen.

Opening a CrystalMaker FileIf CrystalMaker is still running, open Spinel using the File > Open command. Otherwise, locate the “Spinel Tutorial Crystal” file on your hard disc and double-click its icon: CrystalMaker is automatically launched, and the crystal displayed—just as it was before.

Recent Files: A quick way of opening a recently-used CrystalMaker file is to click its thumbnail in the Recent pane of the Overview window, or to use the File > Open Recent submenu.

Resize The PlotIn general, there are four ways of resizing a Graphics window:

• Click the window’s zoom box (Mac) or its maximize button (Windows)

• Click and drag the window’s resize box (Mac) or its frame edge (Windows)

• Use the Tools palette’s window size buttons to toggle between “standard” and “full screen” modes. The full screen mode provides maximum plot area, and is good if you want to present your structure, or show an animated sequence of structures or views. In this mode, unnecessary clutter is hidden (move the mouse to the top or bottom of the screen to show the menubar or the dock/taskbar).

• Choose the Window > Set Plot Size command and enter an explicit size for the Graphics pane.

The structure is re-drawn when you resize the Graphics window.

Section B Displaying a Crystal 14

Changing the Plot RangeLooking at the ball-and-stick model plotted in Tour A, you may notice that some metal atoms are not shown fully bonded; the oxygen atoms to which they should be bonded lie outside the initial plot range (one unit cell). We can plot these missing oxygen atoms by specifying a wider plot range, say from –0.1a to +1.1a parallel to the x, y, and z crystallographic axes.

1 Choose the Transform > Set Range command. The Plot Range window appears.

2 The first text field is for xmin: the minimum x fractional coordinate for atoms to be plotted. Type –0.1 in this box.

3 Press the tab key to move to the next field (xmax). This represents the maximum x fractional coordinate for atoms to be plotted. Type 1.1 in this box.

4 Apply the same range (–0.1 to +1.1) for the y and z axes, pressing tab to move between fields.

5 Click the Apply button to replot your model with extra atoms and bonds. You can now close the Plot Range window.

The Plot Range window

Expand Range: A quick way to expand the plot range along all axes is simply to click the Expand button.


Changing The Background ColourThe default background colour for the Graphics window is black, but this can easily be changed to another colour, a gradient, or a background picture.

1 Use the Model > Model Options command to display the Model Options window.

2 Click the Background tab to display its pane:

3 Ensure that the Plain Background radio button is selected (as shown above), and then click the Colour button.

A colour picker appears, prompting you for a new background colour.

4 Choose a new colour using the colour picker; the Preview rectangle should update to show the colour choice.

5 Click the Apply button at the bottom of the Model Options window to apply your new background colour to the structure. (N.B., any changes you make in this window are not retained, unless the Apply button has been clicked.)

6 Close the Model Options window by clicking its close box.

The Background pane of the Model Options window

Save Colours: The Mac colour picker lets you save your favourite colour “swatches” by dragging them to a panel at the bot-tom of the window.


Rotating The StructureCrystalMaker lets you rotate a structure in real time, with the mouse:

1 Ensure that the Rotate tool is active by clicking its tool button (top left-hand corner of the Tools palette).

2 Move the mouse pointer over your structure. If the window is active, then the cursor changes to an open hand: this indicates that interactive rotation is possible.

3 Click and hold the mouse button down. Drag the mouse down the screen so that the crystal rotates.

To control the rotation we need to understand how mouse movements relate to screen rotation axes. CrystalMaker uses a set of orthogonal axes, which we’ll label XYZ. These should not be confused with your structure’s crystallographic axes (whose orientations are indicated by the axial vectors in the bottom left-hand corner of the screen).

CrystalMaker’s screen axes remain fixed, relative to the screen: the X-axis runs left-to-right; Y runs from the bottom of the screen to the top, and Z is out of the screen, towards you:

Y

XZ

Z-rotation

To rotate about the screen X-axis:

• Drag the mouse vertically, up or down the window

To rotate about the screen Y-axis:

• Drag the mouse horizontally, left-to-right or right-to-left, across the window

To rotate about the screen Z-axis:

• Hold down the shift key then drag the mouse around the edge of the window, in a clockwise or anti-clockwise path.

Note that you’re not just restricted to dragging vertically or horizontally: If you drag the mouse diagonally, both X- and Y-rotations occur.

CrystalMaker screen axes: arrows indicate the sense of

positive rotation

Rotation tools in the Tools palette.

Rotate Tool

Rotation Pad

Toggle Z-Rotation: You can switch from XY to Z rotation (and vice versa), without releasing the mouse button: just hold down, or release the shift key on your keyboard and continue moving the mouse.


Specifying A Rotation AngleMouse-driven, “trackball” rotation is useful, but not always very precise. We shall use the Tools palette’s rotation pad to rotate the crystal through exactly 30° about the screen Z axis.

=

–Z –X +Z

–Y +Y

+Z +X –Z

7 8 9

4 6

1 2 3

1 A default rotation angle is displayed at the centre of the rotation pad. This angle can be changed, by selecting a new angle from a popup menu.

2 Click on the angle, and select 30 from the popup menu. The angle displayed in the centre of the rotation pad should now read 30°.

3 Click one of the +Z buttons in the rotator pad (or press 1 or 9 on your numeric keypad). The crystal rotates about an axis out of the screen.

Tools palette Rotation Pad: The sense of rotation and

corresponding keys on a numeric keypad


Defining a View DirectionAnother way of changing a structure’s orientation is by specifying a crystallographic view direction: making a direction inside the crystal parallel to the screen Z axis. CrystalMaker lets you specify your view direction using one of two kinds of vectors:

• A lattice vector U a + V b + W c (a, b, c, are the axial vectors), which is abbreviated as [UVW];

• The normal to a lattice plane. This is is abbreviated N(hkl), where h, k, and l are the Miller Indices of the lattice plane.

Let us view the spinel structure down the [111] lattice vector:

1 Choose Transform > Set View Direction to display the View Direction sheet (Mac) or dialog (Windows).

2 Ensure that Lattice Vector radio button is selected.

3 Enter 1 in each of the three Indices fields.

4 Click OK to continue.

The window vanishes and the crystal is replotted—viewed along the [111] lattice vector.

Preset View Directions: A faster way to set the view direction is to use the Presets popup, which you can display by clicking its popup menu button, on the right-hand side of the three text fields. Alternatively, you could use the View direction popup menu button in the Window toolbar.

Set View Direction window. A [111] lattice vector has

been entered as the new view direction


Changing the Crystal ModelCrystalMaker is not limited to ball-and-stick plots. The Model menu provides six different plot types: Ball and Stick, Space Filling, Polyhedral, Wireframe, Stick and Thermal Ellipsoid.

A B

C D

For each plot type, you can also choose whether to display:

• unit cell outline

• axial vectors (parallel to the crystallographic xyz axes)

• surface overlay• Experiment with different plot types by selecting their names from the

Model menu.

(Note that the Thermal Ellipsoid item cannot be selected, because we have not specified the requisite data—atomic displacement parameters—for this structure.)

Representations of spinel: (A) Ball-and-stick;

(B) Space-filling; (C) Polyhedral;

(D)Surface overlay


Rendering ModesSo far the structure has been displayed in Crystal Maker’s Colour mode. CrystalMaker uses ambient and point light sources, calculating the intensity of light reflected from each pixel using reflection coefficients to give a photo-realistic effect.

If you wish to preview the results from a greyscale laserprinter, you may find it helpful to switch to Greyscale mode. You’ll get the same high-quality graphics, but in shades of grey.

Alternatively, for simple “line art” diagrams—perhaps for publication in a journal—the Black & White mode is appropriate.

1 Use the Rendering menu to switch between Rendering modes.

2 When you’ve finished, switch back to Colour, for the next part of the tutorial.

Photo-rendered model (left) and stylized version (right)


Atom StylesWe shall now investigate the range of atom styles available.

1 If necessary, choose Ball-and-Stick from the Model menu.

2 Display the Model Options window (Model > Model Options).

3 Click the Atoms tab to display the Atom Options pane.

A list of all the sites in the asymmetric unit is shown, grouped by element. You can open or close the element groups, to show individual sites. For each element and site row the corresponding atom sphere, thermal ellipsoid and polyhedral styles are previewed.

You can change a style by clicking it and selecting a new style from a popup menu.

4 Experiment with different atom styles for each site.

5 Click the Apply button to replot your structure with the new atom styles.

Choosing a new atom style


Bond StylesWe shall now select different bond styles for different bond types. We have a choice of photo-realistically rendered cylinders, plainer colour- or pattern-filled cylinders, or various line styles.

1 Click the Bonds tab in the Model Options window to display the Bond Options pane.

A list of bonds appears, including our new Al–O and Mg–O bonds, and showing their current bond styles and colours.

2 To edit the Al–O bond style, click on bond style and choose a new style from the popup menu that appears.

3 Click the Apply button to replot the structure with the new bond style.

Choosing a new bond style


Polyhedral StylesWe shall now emphasize the different Mg and Al sites in spinel by assigning them different polyhedral styles.

1 Use the Model > Polyhedral command to replot your structure as a polyhedral model.

2 Open the Model Options window (Model > Model Options).

3 Click the Atoms tab to display the Atom Options pane. Notice the scrolling list with icons for sphere, ellipsoid and polyhedral styles.

4 Locate the Al element row. Click, and hold down the mouse button on the polyhedron icon. A popup menu of different polyhedral styles appears.

5 Select the Stripe-Fill Solid entry.

6 Now click the Mg polyhedron icon and select the Plain Solid style from the popup menu:

7 Ensure that the Oxygen (O) polyhedral style is set to Blank: a red cross should be shown.

8 Click the Apply button to replot your structure:

Choosing a new polyhedral style

Spinel plotted as a polyhedral model


Site BrowserThe Site Browser provides a key to the atoms in your plot. It lists all sites in your structure, grouped by element type. You can change site and element colours, apply labelling, or hide sites.

Changing an atom’s colour:

1 Ensure that your structure is plotted in colour (Rendering > Colour) and as a Ball & Stick model (Model > Ball & Stick).

2 If the Site Browser is not visible, make the window Sidebar visible (Window > Sidebar > Show Sidebar), then ensure that this contains the Site Browser (Window > Sidebar > Site Browser).

3 Locate the Al element row, and click its colour button. The colour picker appears, prompting you for a new element colour.

4 Choose a new colour from the colour picker and click its OK button to continue. The crystal is replotted using your new colour.

Isolating atoms by type:

5 Move to the Site Browser and locate the O element row.

6 The third column (“Vis”) has checkboxes, to control visibility of atoms and element groups. Click the O element Vis checkbox to hide all O atoms:

7 To bring back the hidden atoms, click the O element Vis checkbox again. The structure is replotted, with the oxygen atoms visible.

Labelling groups of atoms:

8 Move to the Site Browser and locate the O element row.

9 Click on the Lbl checkbox to label all oxygen atoms:

10 To delete all the atom labels, uncheck the O Lbl checkbox.

It is also possible to label individual atoms and to control what kind of information appears in atom labels. These options are explored in the User’s Guide, Chapter 7: Models. Remember to save your spinel crystal file before you move to the next section! You might want to take a break now

Using the Site Browser to hide all oxygen atoms

Using the Site Browser to label all oxygen atoms

25

CProbing the Crystal

CrystalMaker lets you measure and edit your structure interactively, and lets you export your finished model to the web.In this final section, we’ll investigate ways of probing our crystal: using screen tools to learn more about its structure & bonding. We’ll export data to a text file, and publish a web page.

Tools PaletteCrystalMaker’s Tools palette comprises lots of different buttons, organized by function, into various groups. Buttons for manipulation, selection and measurement are located at the top of the palette, with screen size, scaling and rotation buttons towards the bottom.

Manipulation

Selection

Measurement

Screen Size

Scaling

Rotation Pad

Rotation Mode

Organisation of the Tools Palette

Section C Probing the Crystal 26

Zooming an Area of InterestWe’ll start by focusing on the bonding environment around aluminium.

1 If the spinel structure is not already open, the file you saved earlier Ensure that the structure is plotted in colour, as a ball-and-stick model.

2 Locate an aluminium (Al) atom which has some bonds plotted. (You can identify atoms by their colours, as listed in the Site Browser.)

3 Choose the Magnify tool from the Tools palette. (If the Tools palette isn’t visible, choose Window > Palettes > Tools to make it visible.)

4 Place the mouse pointer over an aluminium atom and click to zoom.

5 Continue zooming in on the aluminium atom until it, and its bonded atoms just fill the Graphics window.

Atom InfoNext, we’ll use the Info tool to display some information about the bonding around an aluminium atom in the spinel structure.

1 Choose the Info tool from the Tools palette.

2 Click on your chosen Al atom. The atom is highlighted, and an info tag appears displaying the site label, element type and atom number.

3 Click on the small info button on the right-hand side of the info tag.

4 Information about the selected atom and any bonded atoms, is now displayed in the Log pane of the Overview window.

Using the Info Tool to get information about an atom

Reverse Zoom: You can zoom out with the Magnify tool by holding down the shift or option/alt keys as you click.


Measuring Distances and AnglesWe shall now measure some distances and angles between an aluminium atom and its bonded neighbours.

Measuring a bond distance:

1 Choose the Bond Distance tool from the Tools palette.

2 Click on the aluminium atom, to highlight it.

3 Click on an oxygen atom bonded to the highlighted Al. The distance between the centres of the two clicked atoms is displayed.

4 Inspect the Log pane of the Overview window. The bond distance is printed here, together with its vector representation, as components of the a, b, and c axial vectors.

Measuring a bond angle:

5 Choose the Bond Angle tool .

6 Click on an oxygen atom, followed by an aluminium atom, followed by a second oxygen atom.

7 Notice that the included angle, as measured in three dimensions, is displayed beside the selected atoms, and also printed in the Log.

Measuring a distance parallel to the screen:

8 Choose the Distance tool from the Tools palette.

9 Click in the Graphics pane and release the mouse button. The clicked point is marked with a cross.

10 Now move the mouse, keeping it within the Graphics pane. As the mouse moves, a line is drawn connecting it to the first clicked point, with the distance shown.

11 Click another point in the Graphics pane. The distance measurement is now frozen.

To rescale the zoomed structure:

12 Click the Autoscale button in the Tools palette. The structure is replotted so that it fits neatly within the Graphics pane.

Measuring a bond angle with the Bond Angle tool


Working with Lattice PlanesCrystalMaker allows you to display a lattice plane slicing through a structure. You can define the orientation of the plane, move it with the mouse—and use it as a guillotine to slice away part of the structure.

To display a lattice plane:

1 Choose Transform > Lattice Plane > Edit. The Lattice Plane window appears:

2 Ensure that the Miller indices are set to 1 1 1.

3 Click the OK button to continue. The structure is replotted with a translucent plane slicing through the centre of the unit cell.

Notice that, by default, the lattice plane is shown centred, relative to the crystal model. The Miller Indices of the lattice plane define its relative orientation, not its absolute position. We’ll experiment with moving the lattice plane through the structure in the next section.

Moving a lattice plane through the structure:

4 Choose the Lattice Plane tool from the Tools palette.

5 Click in the Graphics pane, and drag with the mouse. The plane moves forwards or backwards along its normal.

Hiding a lattice plane:

6 Choose Transform > Lattice Plane > Hide. The structure is replotted without the lattice plane.

The Lattice Plane window

A (111) plane slicing through a unit cell of spinel

Fixed in Space? There is a common misconception that Miller indices some-how fix a lattice plane in space, so that, for instance (111) must pass through corners of the unit cell!

This is not true: the (hkl) indices merely give the relative orientation of a plane (and its d-spacing, if multiple planes are considered).

So a lattice plane can be positioned anywhere along its plane normal, without its indices chang-ing!


Angles between Planes & VectorsWe’re not limited to measuring angles between atoms. You can also measure angles between specified lattice plane normals, and/or lattice vectors.

We’ll measure the angle between the normal to our (111) plane, and the [001] direction (the crystal’s z axis).

1 Choose the Transform > Calculate Angle command to display the Calculate Angle window:

2 Enter the indices 1 1 1 in the Direction 1 fields, and specify that this is a Plane Normal, using the radio buttons below. Direction 1 now represents the normal to the (111) plane.

3 Enter the indices 0 0 1 in the Vector 2 fields and specify that this is a Lattice Vector, using the radio buttons below. Direction 2 now represents the [001] lattice vector. The angle between the two directions is displayed at the bottom of the window.

4 Click the Calculate button to print a summary of the indices and calculated angle in the Log.

5 Hide the Calculate Angle window by clicking its close box.

Brush Up Your Crystallography: If you are unfamiliar with the (hkl) notation for lattice planes, or the [UVW] notation for lattice vectors, these are described in Appendix D: Basic Crystallography of the CrystalMaker User’s Guide.

The Calculate Angle window, showing the angle between

a plane normal and a lattice vector


Hiding AtomsEarlier in the tours you defined a plot range (Transform > Set Range) in terms of fractional distances along the crystallographic axes. CrystalMaker’s selection tools give you additional flexibility in modifying this initial plot range, letting you carve out a precise “chunk” of crystal, or “zap” individual atoms.

Hiding Groups of Atoms

The Arrow, Polygon and Lasso tools allow you to select different-shaped regions in your structure.

1 Choose the Arrow tool from the Tools palette.

2 Click in the Graphics pane and, with the mouse button still down, drag over a number of atoms, defining a rectangle. Then release the mouse button.

The structure is replotted. All atoms within your rectangle now have yellow or red haloes, indicating that they are selected.

We’ll now opt to hide all unselected atoms.

3 Choose the Selection > Hide > Unselected Atoms command. The structure is replotted, showing just selected atoms.

4 Choose Selection > Show All to replot the structure with all the original atoms.

Hiding Individual Atoms

A quick way of tidying-up the edges of a structural model is to use the Zapper tool to hide unwanted atoms.

5 Choose the Zapper tool from the Tools palette. The mouse pointer changes to a “lightning bolt”.

6 Click on an atom and watch it vanish in a small explosion.

7 Choose the Selection > Show All command to replot the structure with all atoms shown (alternatively, if you have only zapped one atom, you can use the Edit > Undo command).

Isolating a layer of oxygen atoms in the spinel structure.

Atom layer selected (left); unselected atoms hidden

(right)


Local Coordination EnvironmentsWe’ve introduced you to some powerful selection tools and, with a bit of work you have the power to select any region inside a crystal model. There is a shortcut, however, which might make life easier if you’re interested in a spherical selection.

CrystalMaker allows you to visualise a spherical cluster of atoms (or even a coordination “shell”) around a central atom. We’ll take advantage of this feature to investigate the bonding around an aluminium atom in spinel.

1 Choose: Transform > Define Cluster. The Define Cluster window appears.

2 Ensure that the Around Site radio button is selected.

3 Choose Al from the popup menu. Note that the site label appears in a second popup menu. As there is only one Al site in this structure, we don’t need to change this.

4 We wish to display all atoms that lie within 2.5 Å of this site, so you should ensure that the Inner Radius field is set to zero and the Outer Radius is set to 2.5 Å, as shown below:

5 Click the OK button to continue. The structure is replotted, showing just the atoms around a central Al; in our case a single AlO6 group is displayed.

Defining a cluster around an Al site.


Local EmbellishmentsWe shall use our AlO6 cluster to experiment with individual atom and bond styles.

1 Select the central Al atom, by clicking on it with the Arrow tool so it appears highlighted.

2 Go to the Selection menu and locate the Atoms > Style sub-menu. Choose a new style from this menu; the central Al atom will be redrawn with the new atom style.

3 Using the method above, choose a new atom style for one of the oxygen atoms in the cluster.

We’ll now change the appearance of the bond between your two “custom” atoms:

4 Select the custom oxygen atom by clicking on it with the Arrow tool.

5 Hold down the shift key on your keyboard and click on the (custom) central Al atom. Both the custom atoms should now be shown highlighted (selected).

6 Choose the Selection > Bonds > Style command. The Bond Style dialog appears, prompting you to choose a new bond style and colour.

7 Choose the dashed-line bond style from the popup menu, and use the colour button to change the line colour to black.

8 Click the OK button to replot your structure with the custom bond style.

An AlO6 group with custom atom and bond styles.


Generating a Distances & Angles FileIf you are interested in recording the bond lengths and angles for all sites in the crystal, you can use CrystalMaker to produce a detailed listing which will be saved as a text file. The file contains coordinates of all the atoms in the unit cell, plus bond angles and lengths for each of the atoms in the asymmetric unit. You can look at the bonds file using any word-processor or text editor. The format of the “Distances & Angles” file is detailed in the User’s Guide, Chapter 11: Importing & Exporting Data.

1 Choose the File > Export > Distances & Angles command. A standard file dialog appears, prompting you for the name of the output file.

2 Use the dialog to specify a filename and location, then click the Save button to continue. CrystalMaker generates a list of atoms and bonds, and saves these to disc.

3 Try opening the file using a text editor program such as TextEdit (Mac) or Notepad (Windows).


Publishing a Web PageJust before we leave, we’ll try one more thing: we’ll build a web page summarising details about the spinel structure and including a screen image. You could use the web page to publish your structure on the internet…

1 The image for our web page will be generated at the same size as your screen image, so you may wish to resize your Graphics Window so the web image won’t be too large.

2 Choose the File > Export > Web Page command. A standard file dialog appears, prompting you to specify a name and location for your web page.

3 Click the Save button to continue. CrystalMaker generates an HTML file (a plain-text document) containing your notebook information, plus cell parameters, spacegroup and the coordinates of atoms in the asymmetric unit. CrystalMaker also generates a compressed image, using the cross-platform JPEG format.

4 Locate your new web page and try opening it in your favourite web browser.

A web page generated by CrystalMaker for spinel


SummaryYou’ve now reached the end of the CrystalMaker tutorial. Well done! You’ve seen how to build a crystal, from scratch; define bonding (and hence coordination polyhedra), display an extended structure, and use selection tools to isolate regions of interest. You’ve explored different representations of the structure, and found how to customize atomic radii and colours. You measured interatomic distances and angles, and found out how to export these data, in a Distances & Angles text file. Finally, you brought data and graphics together, in the form of a web page.

Dynamic VisualizationThere’s much more to CrystalMaker than just the nuts-and-bolts of building structures. The program also features rapid visualization of “raw data” files, with high-quality graphics and video, including the ability to create multi-structure animations.

Animation is a great way to visualize relationships between structures, transformation behaviour within the same structure, or for assessing the trajectory (successive frames) of a computer simulation. Remember that crystal and molecular structures are not dusty, static models: they are dynamic systems in their own right, and your visualization software, CrystalMaker, is equipped to show this…

Learning ResourcesFor more detail on the various features that you’ve used, and to learn about new features not discussed in this tutorial, please refer to the CrystalMaker’s User’s Guide (Help > CrystalMaker User’s Guide). This is the definitive reference to the program, and comes with an index, as well as being fully searchable (try the Search command in your PDF reader).

For a quick, general reference, use Online Help (Help > CrystalMaker Help).

We have also provided some video guides to common workflows, which you can access via the Help > Video Tours command, or directly, by visiting:

http://crystalmaker.com/crystalmaker/tours

We hope you enjoy using the program!

CrystalMaker Software LtdCentre for Innovation & Enterprise

Oxford University Begbroke Science ParkWoodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK

http://crystalmaker.com

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