CrystalMaker Online Help

Edit Bond Specifications Dialog

This dialog lets you define bonds between different kinds of atoms.

The Edit Bond Specifications dialog (Edit > Bond Specs) is the starting point for defining bonding, and hence polyhedra, for your structure.

You can access this dialog in one of two ways:-

Select the Edit > Bond Specs menu command;
If the Edit Crystal dialog is still open, click the Bonds button

Adding a New Bond Specification

On the left-hand side of the Edit Bond Specs dialog are two scrolling lists of element symbols, corresponding to the element types contained in your structure. You use these to specify the atoms on either side of a bond:-

Click on an atom in the From Atom list, then click on an atom in the To Atom list.
Now specify the maximum bond distance: either click the Define radio button, and type a distance; or ensure that the Calculate from radii radio button is checked (this tells CrystalMaker to use an appropriate maximum bond distance, which is calculated as 1.15 multiplied by the sum of the radii for the relevant elements).
Click the Add button to add the new bond specification to the list on the right-hand side of the dialog.

Editing an Existing Bond Specification

The existing bond specifications are listing on the right-hand side of the dialog. Clicking on an entry causes the relevant "To" and "From"atoms to be highlighted in the lists on the left-hand side of the dialog, and the maximum bond distance is displayed in the Define box. You can edit any of these settings, then click the Add button to add the (changed) specification to the list.

Please Remember: You must define bonds before you can plot polyhedra!

Warning: CrystalMaker allows a maximum of 12 bonds per atom, which represents the maximum range of coordinations found in most compounds (e.g., the densest, close-packed structures have coordination numbers (CN) of 12; most compounds have lower CN's). However, if you define a very large maximum bond distance, CN's greater than 12 (hence highly unrealistic!) may result. The program will then ignore all but the 12 shortest bonds. You should then reduce the maximum bond distance and replot the structure.

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