Tool: Cage Builder

Cage Builder creates polyhedral cages composed of hexagons and pentagons. Atomic models can be placed on the cages to create oligomeric molecular assemblies using the sym command. See also: hkcage

The Cage Builder tool can be opened from the Higher-Order Structure section of the Tools menu and manipulated like other panels (more...).

• Create polygon [ 5 ][ 6 ] – clicking a number attaches a new polygon with that number of sides to each currently selected polygon edge, or if no such edges exist, creates a single new polygon. The polygons are added as a marker model named Cage. The attached edges are automatically joined. Joined edges are shown in lighter colors than unjoined edges.

Clicking Minimize improves the alignment of joined edges. This is typically done after some rounds of new polygon attachment.

Clicking Delete removes entire polygons that contain any selected edge or vertex.

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Placing Atomic Models on Cages

Copies of atomic models can be placed on the polygons using the sym command.

For example, one might want to put a single copy of the structure at each pentagon (ignoring any other types of polygons). First, the molecular model would need to be positioned as desired relative to one of the pentagons in the cage model. Then, if the molecule model is #2 and the cage model is #1, the following would place a copy of the molecule model at an equivalent position relative to each pentagon:

Command: sym #2 #1,p5

The copies can be removed with sym clear.

Another possibility is to place multiple copies per polygon. For example, after a molecule model #2 has been positioned relative to (1/6) of a hexagon in cage model #1, the following would use C₆ symmetry about the hexagon center to place six copies per hexagon:

Command: sym #2 #1,pn6 surfaceOnly true

The surfaceOnly option specifies creating low-resolution surfaces instead of atomic copies (for faster rendering).

Currently there is no good way to refine the molecular positions to make the interfaces between molecules physically realistic.