CrystalMaker

Interactive Crystal & Molecular Modelling

Tutorial

New Edition: CrystalMaker 9 for OS X and Windows

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
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2016 CrystalMaker software Ltd. All rights reserved.

An authorized user of a valid copy of CrystalMaker may reproduce
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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, Leila Rimmer, Joel Miller, Yoshitaka
Matsushita and Tim Holland.
Last updated: 11 January 2016

Contents

Tutorial Overview...............................................................................5

Section 1: Building an Inorganic Structure.........................................................7

Structural Data.....................................................................................7

Entering Crystal Data..........................................................................8

Changing Atom Colours & Radii......................................................11

Defining Bonds...................................................................................12

Adding Notes.....................................................................................13

Getting Help......................................................................................14

Saving a Crystal File...........................................................................14

Section 2: Displaying a Crystal..........................................................................15

Opening a CrystalMaker File.............................................................15

Resize The Plot...................................................................................15

Changing the Plot Range...................................................................16

Changing The Background Colour.....................................................17

Rotating With The Mouse..................................................................18

Rotating With The Trackpad..............................................................19

Specifying A Rotation Angle..............................................................20

Defining a View Direction.................................................................21

Changing the Crystal Model..............................................................22

Atom Styles........................................................................................23

Bond Styles.........................................................................................24

Polyhedral Styles.................................................................................25

Site Browser........................................................................................26

Section 3: Probing the Crystal...........................................................................27

Tools Palette.......................................................................................27

Zooming an Area of Interest..............................................................28

Atom Info Tips...................................................................................28

Measuring Distances and Angles........................................................29

Working with Lattice Planes..............................................................30

Angles between Planes & Vectors.......................................................31

Hiding Atoms.....................................................................................32

Local Coordination Environments.....................................................33

Local Embellishments........................................................................34

Generating a Distances & Angles File................................................35

Publishing a Web Page.......................................................................36

Summary............................................................................................37

Dynamic Visualization.......................................................................37

Learning Resources.............................................................................37

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 CrystalMakers capabilities:-

Build a crystal structure using its spacegroup, cell parameters and

asymmetric unit; generate bonding and display a unit cell.
Expand the plot range, locate missing bonds and explore rendering
modes and model types.
Measure the structure, display coordination clusters and export data;
combine graphics and data by publishing a web page.

We recommend that you follow all the steps (indicated by the numbered
boxes, 1 )in order to build up your understanding.

Building 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). Well 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 Data
Building a crystal doesnt 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 unitso
you wont 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, well build a structural model of spinel, MgAl2O4, an
important oxide mineral. Here are the essential data well need:
Structural data for spinel

Crystal system:
Cubic
Spacegroup: F d 3 m (origin choice 2)
Unit cell dimensions:
a = 8.08
Fractional coordinates of atoms in the asymmetric unit:

element

Mg

0.125

0.125

0.125

Al

0.500

0.500

0.500

0.262

0.262

0.262

Well start by entering these data into the program, using the Crystal Editor.

Entering Crystal Data

1

Choose the File > New Crystal command.

The Crystal Editor appears as a sheet (Mac) or dialog (Windows):

The Crystal editor

Whats a Lattice? If you are unfamiliar with the concept of lattices

and unit cells, please refer to the
Basic Crystallography appendix, in
the CrystalMaker Users Guide.

If the Spacegroup field isnt 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.
Wheres 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 spacegroups, we need to explicitly specify the origin setting were using, so that our atomic coordinates
are correctly positioned relative to the symmetry elements. This explains why weve added [origin
2] here.

If youve 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; = = = 90).
Press the tab key on your keyboard to move to the a field and type: 8.08.
The editor window should resemble the following:
4

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

Crystallographic Units: Remember to use ngstrm () units for

unit cell dimensions. 1 = 10-10m
= 0.1nm.

Section 1: Building an Inorganic Structure

5 We shall now add three sites in the crystals 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 to create a new site.

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

Press the return key to highlight the site lable (or simply click on the
label to highlight it). Type a new label (up to six characters with no spaces)
well choose: Al(1). Then press the tab key to move to the next editable field.
7

Well assume that this structure is ordered, so we only need to enter a

single site occupancy value. Type Al in the site occupancy field.
8

Enter values of 0.5 in the x, y, and z fields, pressing the tab key to
move between fields (ignore the U11, U22 fields). Your editor window
should now look like this:
9

Defining our first site

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 +
button to create a new list entry or, to delete an entry, select that row and
click the button.

Section 1: Building an Inorganic Structure

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

13

Click the OK button in the bottom right-hand corner of the window.

14

The Crystal Editor 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.
One unit cell of spinel, displayed in
CrystalMaker.

10

Section 1: Building an Inorganic Structure

Changing Atom Colours & Radii

If you enter an element symbol that CrystalMaker recognises, the program
will automatically assign colours and radii to all atoms with that symbol.
Customizing Elements: The elements that CrystalMaker recognizes are listedwith their colours and radiiin the Element Editor (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.

Part of the Site Browser,

showing atom types, colours
and atomic radii

If you wish to include other atom types in your crystal, or would like to
override CrystalMakers default settings, you can explicitly define atom
colours and radiifor the current structureusing the Site Browser, which
can usually be found in the Graphics windows Sidebar.

1 If the Site Browser isnt visible, use the Window> Show Sidebar command
to show the Sidebar. If for some reason the Site Browser still isnt visible,
choose the Window > Sidebar > Site Browser command.
2 Well 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.

Well now edit the atomic radii, so we need to look at the radius
column, which is labelled r [] to emphasize that radii are measured here in
ngstrm units.
4

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.

Section 1: Building an Inorganic Structure

11

Defining Bonds
We 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 Bond Editor.
1

Choose the Edit > Bonding command. The Bond Editor appears.

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

3 We require AlO 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 AlO bonds,
but instead well ask CrystalMaker to choose sensible values, based on
existing atom data built into the program. (CrystalMaker automatically
calculates maximum bond distances as 1.15 (rA + rB) where rA and rB are
the radii of the from and to atoms.)
The maximum bond distance should be displayed in the Bmax field and the
resulting coordination environments encompassed by this bond specification
and indicated on the right-hand side, i.e.,

Al will be 6-fold coordinated by O;

O will be 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.
4 Repeat steps 23, but requesting MgO bonds. When you have finished,
the window should resemble the one shown below:
The Bond Editor, showing AlO and
MgO bond specifications

5 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 hidden. We shall investigate ways of fixing this in Section B!

12

Section 1: Building an Inorganic Structure

Adding Notes
You 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.
2

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

Type some text into the pane.

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

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

Section 1: Building an Inorganic Structure

13

Getting Help
CrystalMaker 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 applications 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 File

Before we do anything else, we ought to save what weve done.
From the File menu, choose the Save command. Note that because this is
a new crystal which hasnt previously been saved, youll be presented with a
standard file navigation dialog.
1

CrystalMaker binary file icon

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! Youve 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).

14

Section 1: Building an Inorganic Structure

Displaying 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. Well use this file in the present tour, to
investigate different crystal models, and to experiment with manipulating the
structure on screen.

Opening a CrystalMaker File

If 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
displayedjust 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 Plot

In general, there are four ways of resizing a Graphics window:

Click the windows zoom box (Mac) or its maximize button (Windows).

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

Click and drag the windows resize box or its frame edge.
Use the Tools palettes 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).

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

15

Changing the Plot Range

Looking at the ball-and-stick model plotted in Section 1, 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.
Choose the Transform > Set Range command. The Plot Range window
appears.
1

The Plot Range window

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

16

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

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

Section 2: Displaying a Crystal

Changing The Background Colour

The 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 Inspector command to display the Model
Inspector.

Click the Background button (

reveal the Background Inspector:
2

) in the Inspectors button bar to

The Background Inspector

(Mac version)

Background Presets: The Background Inspector includes a number of preset colour and gradient
themes that you can immediately
apply to your structure.

3 Locate the Fill Pattern group, ensure that Plain Background is specified (as
shown above) and click the Colour button.

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

4 Choose a new colour using the colour picker; your structure is replotted
with the new background colour.
5

Close the Model Inspector by clicking its close box.

Section 2: Displaying a Crystal

17

Rotating With The Mouse

CrystalMaker lets you rotate a structure in real time, with the mouse or
trackpad (Mac version). Here well investigate using the mouse:

Rotate Tool

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

(top

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.
2

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

Rotation Pad

Rotation tools in the Tools palette.

To control the rotation we need to understand how mouse movements

relate to screen rotation axes. CrystalMaker uses a set of orthogonal axes,
which well label XYZ. These should not be confused with your structures
crystallographic axes (whose orientations are indicated by the axial vectors in
the bottom left-hand corner of the screen).
CrystalMakers 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:

CrystalMaker screen axes: arrows

indicate the sense of positive rotation

r
Z-

ot
at

ion

To rotate about the screen X-axis:

Drag the mouse vertically, up or down the window

To rotate about the screen Y-axis:

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.

18

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 youre not just restricted to dragging vertically or horizontally: If

you drag the mouse diagonally, both X- and Y-rotations occur.

Section 2: Displaying a Crystal

Rotating With The Trackpad

Mac users can use standard multi-touch gestures to rotate (and scale) the
structure.
To rotate about the screen X-axis:

Slide two fingers up or down the trackpad.

To rotate about the screen Y-axis:

Slide two fingers left or right, across the trackpad.

To rotate about the screen Z-axis:

Use a Rotate gesture.

Section 2: Displaying a Crystal

19

Specifying A Rotation Angle

Mouse-driven, trackball rotation is useful, but not always very precise. We
shall use the Tools palettes rotation pad to rotate the crystal through exactly
30 about the screen Z axis.
Tools palette Rotation Pad:
The sense of rotation and
corresponding keys on a numeric
keypad

Z X +Z

+Y

+Z +X Z

9
6

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.

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.
3

20

Section 2: Displaying a Crystal

Defining a View Direction

Another way of changing a structures 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 Ua + Vb + Wc (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).
Set View Direction window.
A [111] lattice vector has
been entered as the new view
direction

Ensure that Lattice Vector radio button is selected.

Enter 1 in each of the three Indices fields.

Click OK to continue.

The window vanishes and the crystal is replottedviewed 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.

Section 2: Displaying a Crystal

21

Changing the Crystal Model

CrystalMaker 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.
Representations of spinel:
(A) Ball-and-stick;
(B) Space-filling;
(C) Polyhedral;
(D)Surface overlay

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 dataatomic displacement parametersfor this
structure.)

22

Section 2: Displaying a Crystal

Atom Styles
We shall now investigate the range of atom styles available.
1

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

Display the Model Inspector (Model> Model Inspector).

Click the Atoms button (

) to display the Atoms Inspector.

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.

Choosing a new atom style for Oxygen

atoms in our structure.

4 Experiment with different atom styles for each site. The structure is
automatically replotted each time.

Section 2: Displaying a Crystal

23

Bond Styles
We shall now select different bond styles for different bond types. We have
a choice of photo-realistically rendered cylinders, plainer colour- or patternfilled cylinders, or various line styles.
1 Switch to the Bonds Inspector by clicking the Bonds button (
Model Inspectors button bar.

) in the

A list of bonds appears, including our new AlO and MgO bonds, and
showing their current bond styles and colours.
To edit the MgO bond style, click on its bond style icon and choose a
new style from the popup menu that appears.
2

Choosing a new bond style

24

Section 2: Displaying a Crystal

Polyhedral Styles
We 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.

Switch back to the Atoms Inspector by clicking the Atoms button in the
Model Inspectors button bar. Notice the scrolling list with icons for sphere,
ellipsoid and polyhedral styles.
3

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

Select the Stripe-Fill Solid entry.

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

Choosing a new
polyhedral style

Spinel plotted as a
polyhedral model

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

You will now have a stylized polyhedral model with plain coloured Mg
tetrahedra and stripe-filled Al octahedra.

Section 2: Displaying a Crystal

25

Site Browser
The 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 atoms colour:
1

Switch to 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.

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:
6

Using the Site Browser to hide

all oxygen atoms

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

Labelling groups of atoms:

8

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

Click on the Lbl checkbox to label all oxygen atoms:

Using the Site Browser 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 Users
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

26

Section 2: Displaying a Crystal

Probing 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, well investigate ways of probing our crystal: using screen
tools to learn more about its structure & bonding. Well export data to a text
file, and publish a web page.

Tools Palette
CrystalMakers 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.
Organisation of
the Tools Palette
Manipulation

Selection

Measurement

Screen Size

Scaling

Rotation Pad

Rotation Mode

27

Zooming an Area of Interest

Well start by focusing on the bonding environment around aluminium.
Ensure that your spinel structure is open, and displayed as a ball-andstick model.
1

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
isnt visible, choose Window> Palettes > Tools to make it visible.)
Reverse Zoom: You can zoom out
with the Magnify tool by holding
down the shift or option/alt keys as
you click.

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

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

Atom Info Tips

Next, well use the Arrow tool to display some information about the
bonding around an aluminium atom in the spinel structure.
1

Choose the Arrow

from the Tools palette.

Move the mouse over the Al atom. The atom is highlighted, and after
a short delay, an Info Tip appears, displaying the site label, its chemical
occupancy (element type) and atom number.
2

Click inside the tip to expand it and reveal more detailed information.

Atom Info Tips displayed in a

collapsed state (left) and expanded
state (right)

Click the Site, Bonds and Angles buttons. You should see detailed data
printed in the Log pane of the Overview window (at the bottom of the
screen).
4

28

Section 3: Probing the Crystal

Measuring Distances and Angles

We 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.

Click on the aluminium atom, to highlight it.

3 Move the mouse over other atoms in your structure. As you move, the
inter-atomic distances are displayed.
4 Click a second atom. The distance measurement is now locked and
data are printed in the Log pane of the Overview window. These include the
distance, plus the bond vector, 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. Click on the last oxygen atom again to lock the
measurement. (Note: the Bond Angle tool also lets you measure torsion angles, by
clicking on a fourth atom.)

Notice that the included angle, as measured in three dimensions, is

displayed beside the selected atoms, and also printed in the Log.
7

Measuring a bond angle with

the Bond Angle tool

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 locked, and is printed to the Log.

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.

Section 3: Probing the Crystal

29

Working with Lattice Planes

CrystalMaker allows you to display a lattice plane slicing through a structure.
You can define the orientation of the plane, move it with the mouseand
use it as a guillotine to slice away part of the structure.
To display a lattice plane:

Choose: Transform > Set Plane Properties. The Lattice Plane window
appears:
1

The Lattice Plane window

Ensure that the Miller indices are set to 111.

3 Click the OK button to continue. The structure is replotted with a

translucent plane slicing through the centre of the unit cell.

A (111) plane slicing through

a unit cell of spinel

Fixed in Space? There is a common misconception that Miller

indices somehow fix a lattice plane
in space, so that, for instance (111)
must pass through corners 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. Well 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.

This is not true: the (hkl) indices

merely give the relative orientation
of a plane (and its d-spacing, if multiple planes are considered).

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

So a lattice plane can be positioned

anywhere along its plane normal,
without its indices changing!

Hiding a lattice plane:

30

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

Section 3: Probing the Crystal

Angles between Planes & Vectors

Were not limited to measuring angles between atoms. You can also measure
angles between specified lattice plane normals, and/or lattice vectors.
Well measure the angle between the normal to our (111) plane, and the
[001] direction (the crystals z axis).
1

Choose: Measure > Angle to display the Angle Calculator:

The Calculate Angle window,

showing the angle between
a plane normal and a lattice
vector

2 Enter the indices 111 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.

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.
3

Click the Calculate button to print a summary of the indices and

calculated angle in the Log.
4

Hide the Angle Calculator 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 Users Guide.

Section 3: Probing the Crystal

31

Hiding Atoms
Earlier in the tours you defined a plot range (Transform > Set Range) in
terms of fractional distances along the crystallographic axes. CrystalMakers
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.

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.
2

The structure is replotted. All atoms within your rectangle now have yellow
or red haloes, indicating that they are selected.
Well now opt to hide all unselected atoms.
Choose the Selection > Hide > Unselected Atoms command. The structure
is replotted, showing just selected atoms.
3

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

Isolating a layer of oxygen atoms

in the spinel structure. Atom layer
selected (left); unselected atoms
hidden (right)

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
changes to a lightning bolt.
6

from the Tools palette. The mouse pointer

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).

32

Section 3: Probing the Crystal

Local Coordination Environments

Weve 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 youre interested in a
spherical selection.
CrystalMaker allows you to visualise a spherical cluster of atoms (or even
a coordination shell) around a central atom. Well 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.

Ensure that the Around Site radio button is selected.

Select Al in the first list, followed by the corresponding site, Al(1) in the
second list.
3

4 We wish to display all atoms that lie within 2.5 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 , as shown below:
Defining a cluster around
an Al site.

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.
5

Section 3: Probing the Crystal

33

Local Embellishments
We 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.

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.
2

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

Well 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.

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).
5

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

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.

34

Section 3: Probing the Crystal

Generating a Distances & Angles File

If 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
Users Guide, Chapter 11: Importing & Exporting Data.
Choose the File > Export > Distances & Angles command. A standard file
dialog appears, prompting you for the name of the output file.
1

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).

Section 3: Probing the Crystal

35

Publishing a Web Page

Just before we leave, well try one more thing: well 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 wont 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.

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

A web page generated by

CrystalMaker for spinel

36

Section 3: Probing the Crystal

Summary
Youve now reached the end of the CrystalMaker tutorial. Well done!
Youve 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. Youve 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 Visualization
Theres 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 multistructure 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 Resources
For more detail on the various features that youve used, and to learn about
new features not discussed in this tutorial, please refer to the CrystalMakers
Users Guide (Help > CrystalMaker Users 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!

Section 3: Probing the Crystal

37

CrystalMaker
S O F T W A R E
CrystalMaker Software Ltd
Centre for Innovation & Enterprise
Oxford University Begbroke Science Park
Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK

1994 2016
22 Years of

Innovation

http://crystalmaker.com