CrystalMaker Help > Guide > Building

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Displaying Thermal Ellipsoids

CrystalMaker allows you to display thermal ellipsoids, using the Thermal Ellipsoid model type (Model menu). This commmand is enabled if you have thermal ellipsoid data for your structure - and you are working in crystal mode. Thermal ellipsoids cannot be plotted for 'molecule' mode.

Loading Thermal Ellipsoid Data

CrystalMaker can import thermal ellipsoid data from a number of different text file formats, including CIF, GSAS, PDB, SHELX, and CrystalMaker Text.

Editing Thermal Ellipsoid Data

You can edit thermal ellipsoid data using the Edit Crystal sheet/dialog (Edit > Structure).

By default, the Edit Crystal sheet/dialog shows only atomic coordinate data. However, you can customize the atoms list using the Show popup menu. This has options to display isotropic displacement parameters, anisotropic parameters, all displacement parameters or, if your screen is wide enough, all data.

To add new data, you will need to click the Use Displacement Parameters checkbox, and then enter new values, as well as specifying the type of displacement parameter required (Biso, Uij or Bij).

Entering Thermal Ellipsoid Data in a Text File

You can export your structure to a CrystalMaker Text file, then use the UISO, UANI or BANI tags to define entries for isotropic, or anisotropic displacement parameters.

Please see the CrystalMaker Text reference for more details, or refer to the User's Guide.

Thermal Ellipsoid Display Styles

Thermal ellipsoids are displayed according to the element and site settings listed under the Atoms pane of the Model Options window (Model > Model Options). You can choose to display different ellipsoid styles for different elements and/or sites.

CrystalMaker provides a wide range of styles, including "traditional" ORTEP black-and-white styles, stylized colour representations, and photo-realistically-rendered styles with cut-out octants to show the ellipsoid axes, and the option of translucency.

The Atoms pane also lets you can specify the probability value for the ellipsoid surface (the default value is 50% probability).

Displaying Hydrogens as Small Spheres

It is common to represent some sites - such as hydrogen - using small spheres (since the thermal ellipsoids tend to be quite large and obstruct other areas of the plot).

To do this in CrystalMaker, simply locate the Ellipsoid column of the scrolling site list (Atoms pane), and turn off the checkboxes for any relevant elements or sites. Small spheres will then be plotted for these - you can control their radii using the Sphere Radius text field.