Surfcat (msms cat) is used to create groupings of atoms for subsequent surface calculations. The atoms in atom-spec are assigned to a category named category_name. ** In most cases, the categories created automatically when a model is read in are sufficient (see surface), and only the surface command is needed. ** An atom can only be in one category at a time, so it is in the last category it matched. Therefore, a typical strategy for computing a surface is to put all atoms of a model in a category, and then put atoms that should not be surfaced (e.g., ligands, water) in other categories (see the example below). This is a subtractive definition. Of course, a category of interest could also be defined directly.
The surfaces defined by the new categories can be displayed using the surface command.
Surfrepr (msms repr) changes the surface representation of the specified models to the specified style, where possible values for style are:
The model_number(s) should be preceded by #, as in a normal atom specification. If no model numbers are given, all surface models will be affected.
In the following example, the sidechains and backbone of a peptide
are placed in separate categories, and a surface is shown for the
surfcat schain #0
surfcat bbone @n,ca,c,o
Known problem: when a category includes disjoint regions, the surface will be drawn for only one of these regions. For example, the following yields a surface around only one of four heme residues:
open 4hhbTo surface the regions independently, they must be placed in separate categories with msms cat (surfcat):
surfcat hemes :hem
surfcat heme1 :hem.a
surfcat heme2 :hem.b
surfcat heme3 :hem.c
surfcat heme4 :hem.d
See also: surface, surftransparency, the surface attributes panel, the Actions menu