Feature Tutorials

Building Cage Structures in CrystalMaker

Simplifying complex cage geometries using coordination polyhedra

CrystalMaker lets you simplify complex structures by using polyhedral representations to replace groups of atoms and bonds. A question arises when working with empty cage structures, such as in zeolites or buckyball (C-60) compounds. Because the cages are empty, they cannot be automatically displayed as polyhedra. Fortunately, CrystalMaker comes to the rescue, with its Make Polyhedron command, as described in the following tutorial.

C60 cage C60 cage

The latest versions of CrystalMaker for Mac and Windows make it easy to depict cage structures (left) as solid polyhedra (right).

Building a "Solid" Polyhedron

1. Define Selection. One needs to select all atoms in the cage - these will be the vertices of the final polyhedron. For a typical zeolite, one would want to select the tetrahedral sites (Al,Si atoms). In this example, we are selecting carbon atoms in C60. Because the C60 units are not interbonded (in this representation), one can select an entire "molecule" using the Selection > Select > Entire Molecule menu command, resulting in the following display:

C60 cage step 1

2. Make Polyhedron command. Choose the Make Polyhedron command from the Selection menu. The Make Polyhedron sheet or dialog appears:

step 2

Specify an element symbol and site label for the new (centroid) site - it is probably a good idea to use a "fake" element symbol, to make it easier to distinguish this from the other atoms.

One would probably want to specify bond generation (including symmetry-related bonds) and specify that symmetry-related polyhedra are also shown. Note that without bonds, it is not possible to display a polyhedron.

Click the OK button to continue. After a slight pause the structure is plotted. Notice that new sites have been created at the centres of the cages, with bonds to the surrounding "cage" atoms. We can use these to define polyhedra.

step 3

3. Tweak the Polyhedral Plot. It is usually a good idea to check the polyhedral site styles to ensure that only the cages are plotted as polyhedra: use the Model > Model Options command, click on the Atoms tab, and specify blank polyhedral styles for all sites except for the polyhedral centroid.

step 4

Switch to the Polyhedral model type (Model > Polyhedral) to display a solid polyhedron.

step 4

One might also want to edit the Rendering Options for polyhedra to ensure that edges are not drawn - some structures do not have perfectly-flat faces, and so a simple hexagonal face might actually be comprised of (say) a rectangle and two triangles.

To edit rendering settings, choose the Rendering Options command from the Rendering menu. In the window that appears, select the "Reflectance" tab to display the Reflectance Options pane. Next, specify "Polyhedra" in the "Rendering For" popup and choose "none" in the "Show Frame" popup:

step 5

Click the Apply button to replot the structure. We now have nicely-rendered "solid" polyhedral cages.

step 6

The "Coloured Faces" Method

Instead of generating an entire, "solid" polyhedron for the C60 structure, one could instead define planar polyhedra for the cage faces. This allows one to colour the different face types separately - useful for emphasizing symmetry relationships.

One can select a group of atoms that form the vertices of a face, then use the Make Polyhedron command, as in the previous example. One will probably need to repeat this if there are other faces, not related by symmetry. One will end up with a series of "fake" sites at the face centres, as illustrated below:

C60 cage

One can display a polyhedral model with the "fake" face atoms displayed as opaque or translucent planes - and if you use different colours for the different "fake" sites, you can observe the symmetry, as can be seen in the next example:

C60 cage

Important Notes

The Make Polyhedron command is designed for specific cases where the structure contains large, empty cages. For general structure types, use the Edit > Bonding command to specify bonding and polyhedral generation.

Please note that the Make Polyhedron command generates symmetry-related bonds. These are not necessarily the same as the bonds generated by the Edit > Bonding command, which uses atomic distance criteria.

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