CrystalMaker Help > Guide > Building

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Defining Bonds and Polyhedra

Defining the bonding in your structure is an important step as it allows you to view connectivities, space-filling overlap, wireframe display - and coordination polyhedra.

How to Define Bonds

You can define bonds on an atom-by-atom basis, you can request bonds between particular atom types up to a maximum distance, or CrystalMaker can automatically generate bonds for you.

Defining Individual Bonds

You can use the Add/Delete Bond Tool to generate a bond between two specified atoms. With this tool selected, click on two atoms in the structure. If the atoms are already bonded to each other, their bond will be deleted; otherwise, a new bond will be created between them.

If you hold down the shift key as you click the second atom, CrystalMaker will generate similar bonds throughout the plotted structure.

Global Bond Specifications

You can use the Edit Bonding Sheet (Edit > Bonding) to request global bond specifications, on the basis of atom types (element symbols) and their maximum separations.

Automatic Bond Generation

You can use the Transform > Generate Bonds Now command to search through the structure and generate bonds for all atoms whose interatomic separations lie within 15% of the sum of their radii.

You may need to edit atomic radii for this method to work. In some cases you may wish to import a new Element Table (Edit > Elements) - e.g., if you usually work with ionic structures but wish to plot an organic structures, you might want to temporarily use atomic radii corresponding to those found in organic structures.

How to Define Polyhedra

Once bonds have been generated, CrystalMaker will automatically generate coordination polyhedra; these can be displayed using the Model > Polyhedral command. You can customize display styles for individual sites, using the Atoms pane of the Model Options window (Model > Model Options).

Custom-Defined Polyhedra

Instead of relying on (radial) bond specifications, you can display your own polyhedra, using the Make Polyhedron command from the Selection menu. You need to choose which atoms should appear at the vertices of your polyhedron, select them and then choose the Make Polyhedron command. A new site will be generated at the centre of your selection, with bonds to the selected, vertex, atoms. You also have the option of display symmetry-related polyhedra.