CrystalMaker Guide: Atom Specifications

Atoms can be coloured according to their crystallographic site, or by chemical element. Atomic radii can be manually set, or automatically defined using global Element Radius data sets.

Editing Atom Colours &Radii

You can use the Edit > Atom Specs command to define global atom colours and radii for the sites in your structure. The resulting, Edit Atom Specifications dialog lets you colour atoms according to crystallographic site, or by chemical element.

You can also change global atom colours using the Info Window (Windows > Info). The Info Window lists atoms according to their chemical element. Each element row has a coloured bar. If you click this, you are prompted for a new colour, and the stucture is then replotted.

Editing Individual Atoms Colours & Radii

Atoms are normally coloured according to their site settings, but you can override these settings for individual atoms (note that for crystals, regenerating the structure, or changing the plot range, may reset colours back to their default values).

You can change the colour of a selected atom or group of selected atoms using the Selection > Atom Colour command. (To select an atom, click on it with the arrow tool, or draw round it using the rectangle, polygon or lasso tools.)

If you are editing a molecule, you can also change the site type for any selected atoms. This makes it possible to change atom colours, element symbols and radii ­ all in one step. Select the Selection > Atom Type command.

Using Element Colour/Radius Data Sets

CrystalMaker relies on atomic radii for its bond and polyhedral generation routines. However, the radius of a particular atom depends in part on its bonding - which may vary from structure to structure. The default atomic radii used by CrystalMaker correspond to those measured for inorganic crystals. If you are working with different kinds of structures (e.g., organics, or native elements), then these radii are inappropriate.

CrystalMaker's Elements dialog (Edit > Elements) lets you manage the default atomic radii and colours, and to override the current settings. You can manually define colours and radii, or you can import a ready-made set from disc. CrystalMaker (commercial version) is shipped with a number of element radius data sets, including data for organic, inorganic, elements, and other structures; these are located in the Element Tables folder.

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