Msms cat (or surfcat) 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.
Msms repr (or surfrepr) 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.
See also: surface, vdw, the Actions menu