
Concepts introduced: Surface subsets (§6.8)
Start spock and type fetch=12ca.pdb to load the the structure of carbonic anhydrase. Type
makesurf
to build a molecular surface and accept the default value of 65
for the grid resolution. Now, under the Alter
Surfaces
menu, choose ``Find connectivity.'' This option will trace through all
the defined vertices and figure out which vertices are connected to which
others. When done, it will print out a list of independent surfaces and
cavities, and their associated areas and volumes. These surfaces and
cavities are also defined as surface subsets called mainN, or
cavN for surfaces and cavities, respectively, where N is an
integer. You can select these surfaces subsets with the vsub=
surface selection (§6.8). For example, try the command
vc=0,vsub=main0
This will hide the main0 subset. You can also use the macro Color_surface_subsets to color each surface a different color.