The command surfrepr (msms repr) changes the surface representation, whereas surfcat (msms cat) is used to specify sets or categories of atoms that should be grouped for surface calculation purposes. See also: surface, split, transparency, the Actions menu, surface calculation failures and workarounds
Surfrepr changes the representation surface representation, of specified models to the specified style:
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. Possible values for style are:Surfcat creates groupings of atoms for subsequent surface calculations:
- filled or solid (solid surface)
- mesh (the surface polygon edges only are shown)
- dot (the surface polygon vertices only are shown)
The atoms in atom-spec are assigned to a category named category_name. A category's surface can then be displayed with the command surface.
In many cases, the automatic categories suffice and surfcat is not required. Categories are mutually exclusive, that is, an atom can only be in one category at a time. When atoms are placed in a new category, they are subtracted from the category they occupied previously.
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 1gcnIn the next example, the structure has two DNA chains (E and F) and three protein chains (A-C). Automatic categorization would put all of these chains in category main and enclose them in a single surface:
surfcat schain #0
surfcat bbone @n,ca,c,o
surface schainopen 1tup; rainbow chainTo separately enclose the DNA and the protein:
surfacesurfcat dna nucleic acidTo further enclose each protein chain separately:
surf dnasurfcat one :.a & proteinThe “& protein” specifications are needed to exclude nonprotein residues of chains A, B, and C (in this case, several water molecules) from the surface categories.
surfcat two :.b & protein
surfcat three :.c & protein
surf one | two | three