Chimera Commands Index

( surfcat | msms cat ) category_name atom-spec

( surfrepr | msms repr ) style model_number(s)

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 sidechain portion.

open 1gcn
surfcat schain #0
surfcat bbone @n,ca,c,o
surface schain

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 4hhb
surfcat hemes :hem
surf hemes
To surface the regions independently, they must be placed in separate categories with msms cat (surfcat):
open 4hhb
surfcat heme1 :hem.a
surfcat heme2 :hem.b
surfcat heme3 :hem.c
surfcat heme4 :hem.d
surf heme1
surf heme2
surf heme3
surf heme4

See also: surface, surftransparency, the surface attributes panel, the Actions menu