Cage Builder Cage Builder icon

Cage Builder figure

Cage Builder creates polyhedral cages composed of hexagons, pentagons, squares and other polygons. The cages can be decorated with atomic models to create oligomeric molecular assemblies using the sym command (see examples). Cages are created as marker sets. See also: Icosahedron Surface, hkcage, meshmol

There are several ways to start Cage Builder, a tool in the Higher-Order Structure category.

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. Close simply dismisses the dialog, and Help opens this manual page in a browser window.

Clicking Options reveals additional settings (clicking the close button on the right hides them again):

Placing Atomic Models on Cages

Molecules on cage figure

Copies of molecular models can be placed on each polygon 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. Models can be positioned relative to one another “manually” by activating/deactivating them for motion and using the mouse. Then, if the molecule model is #1 and the cage model is #0, the following would place a copy of the molecule model at an equivalent position relative to each pentagon:

Command: sym #1 group #0,p5

The copies can be removed with ~sym.

Another possibility is to place multiple copies per polygon. For example, after a molecule model #1 has been positioned relative to (1/6) of a hexagon in cage model #0, the following would use C6 symmetry about the hexagon center to place six copies per hexagon:

Command: sym #1 group #0,pn6 surface true update true

The additional arguments in the second example specify creating low-resolution multiscale surfaces instead of atomic copies (for faster rendering) and updating their positions when the original copy of the molecular model is moved relative to the cage.

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

UCSF Computer Graphics Laboratory / July 2011