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Finding internal cavities in a molecule

  OBJECTIVE: This tutorial demonstrates how to use connectivity and surface information to find internal cavities in a molecule.

Concepts introduced: Surface subsets (§6.8)

Start spock and type fetch=12ca.pdb to load the the structure of carbonic anhydrase. Type


to build a molecular surface and accept the default value of 65 for the grid resolution. Now, under the Alter tex2html_wrap_inline6800 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


This will hide the main0 subset. You can also use the macro Color_surface_subsets to color each surface a different color.

Jon Christopher
Tue Sep 14 16:44:48 CDT 1999