Feature Tutorials

"ORTEP"-Style Models in CrystalMaker

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CrystalMaker lets you display models in a wide range of different styles. In this tutorial we look at a very special case: depicting thermal ellipsoids using a stylized black-and-white scheme, similar to that generated by the old "ORTEP" program.

Cubane molecule in Photo Colour mode Cubane molecule in Black-and-White mode

A cubane molecule displayed in CrystalMaker using colour and photo-realism (left), and a stylized black-and-white design (right).

Introduction

CrystalMaker, as with many other visualization programs, is designed to take full advantage of your computer monitor and video card, by providing photo-realistic colour graphics. (Actually, CrystalMaker goes beyond many other programs, by also providing high-resolution output, for use in publications and posters.)

Whilst such graphics look very impressive on screen, there are times when a much simpler representation is required, using stylized graphics to show the absolute minimum necessary to show the structural essentials. This is where the full richness of CrystalMaker's Model and Rendering Options comes into force.

Using CrystalMaker, you choose from a wide range of designs for atoms, thermal ellipsoids, bonds and polyhedra. Furthermore, you can display the resulting combinations in a choice of three different Rendering Modes: Colour, Greyscale or Black-and-White.

Tutorial

In this tutorial we'll take a look at producing a stylized black-and-white image of an organic molecule, showing thermal ellipsoids in a traditional manner, akin to that of the old "Oak Ridge Thermal Ellipsoid Program" ("ORTEP"). We'll assume that you have a structure already open on screen, and that thermal ellipsoid data (also known as "atomic displacement parameters") are available.

1. Black-and-White

The first step is to switch from the default, Colour, rendering mode, to Black-and-White. Simply choose: Rendering > Black-and-White. Your background colour is changed to pure white, and simpler styles may be shown for model elements such as atom spheres, ellipsoids or bonds.

2. Thermal Ellipsoid Display

We'll now display thermal ellipsoids for your atoms, using the Model > Thermal Ellipsoid command. (This command will appear greyed out if, for some reason, your structure does not have the requisite thermal ellipsoid data.)

3. Model Options

We shall now adjust the styles used in your model. To do this we require the Atoms pane of the Model Options window: choose Model > Model Options to display the Model Options window, then click on the Atoms tab. You should see a scrolling list of all sites in your structure, grouped by chemical element:

Compression Settings dialog

The Atoms pane of the Model Options window, showing a Hollow Equatorial Octant ellipsoid style for the C sites and a Hollow (sphere) style for the H sites.

Changes can be made to the atom sphere, thermal ellipsoid and polyhedral styles - on a per-element basis or, by clicking on an element row's "disclosure triangle", on an individual-site basis.

  1. Atom Options. If you haven't already done so, ensure that the Model Options window is visible (Model > Model Options) with its Atoms tab open.

  2. Choosing a Default Ellipsoid Style. Click on the Ellipsoid icon shown in the Default row. A popup menu appears, giving a wide selection of different display styles. Choose: Hollow Equatorial Octant. The Default style is updated.

  3. Copying the Default Style. We shall now copy the default ellipsoid style to all other sites in the model. To do this, click the little grey arrow next to the Default ellipsoid icon. (Alternatively, click the Use Default Style button, on the right-hand side of the Atoms list.)

  4. Display Hydrogens as Small Spheres. It is very common to ignore the thermal ellipsoid data for light atoms such as hydrogen, and instead show their positions using small spheres. You can do this by scrolling down to the H element row and unchecking the little checkbox next to the ellipsoid.

  5. Replot your Structure. To apply these changes to your displayed structure, simply click the Apply button, located on the bottom right-hand side of the Model Options window.

4. Bond Styles

We'll now change the styles for all bonds in your structure. We'll follow a similar sequence of steps as for the Ellipsoid options.

Compression Settings dialog

The Bonds pane of the Model Options window, showing a Plain Cylinder style (with white colouring) for all bond types.

  1. Bond Options. Click the Bonds tab to display the Bond options pane.

  2. Choosing a Default Bond Style. Click on the Bond icon shown in the Default row. A popup menu appears, giving a selection of different display styles. Choose: Plain Cylinder. The Default style is updated.

  3. Copying the Default Style. We shall now copy the default bond style to all other bonds in the model. To do this, click the Use Default Style button, on the right-hand side of the Bonds list.)

  4. Replot your Structure. To apply these changes to your displayed structure, simply click the Apply button, located on the bottom right-hand side of the Model Options window.

5. Summary

You should now have a classic "ORTEP"-style black-and-white plot, like the one shown at the top of this page. If you save this structure, you can use it as a template for other structures, via the Window > Synchronize command.

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