The surface command displays molecular surfaces. In Chimera, these surfaces are created with embedded software from the MSMS package, described in:
M.F. Sanner, A.J. Olson, and J.C. Spehner, "Reduced surface: an efficient way to compute molecular surfaces" Biopolymers 38:305 (1996).The probe radius and density of vertices used to compute a molecular surface can be adjusted in the surface attributes panel.
When a model is read in, it is automatically divided into the following mutually exclusive categories:
|category-name||membership rules (applied in the order listed)|
|ions||singleton atoms (not covalently bonded to other atoms) of atomic number ≥ 9, plus covalently bonded groups of ≤ 4 atoms (not counting hydrogens) in the same residues as those singletons|
of the following two, the set with the greater number of residues:
|ligand||single residues or bonded sequences of residues with < 250 atoms and < 1/4 the number of atoms in the largest bonded sequence of residues in the model|
|main||all remaining atoms|
When the surface command is issued with a category-name, the surface is calculated and displayed for the atoms in that category. When the surface command is issued with an atom-spec, the surface is calculated for each entire category that contains any of the atoms in atom-spec, but only the surface corresponding to those atoms is displayed. If both category-name and atom-spec are given, the surface is calculated for the whole category, but only the surface for the specified atoms within the category is displayed. ~Surface undisplays the surface. The default category-name is main (see table), and a blank atom-spec is equivalent to # (all atoms).
Categories can be defined manually when the automatic categories do not give the desired results. For example, one may want surfaces enclosing the individual subunits of a multimeric protein instead of one surface enclosing the multimer as a whole. Sets of atoms (like the subunits) can be separated into different categories with msms cat (surfcat).
Surface is then used to display the surface of interest. The surface representation (solid, mesh, or dot) is controlled with msms repr (surfrepr).
surface #0- display the surface for all categories in model 0
surface- display the surface for category main in all opened models
surface ligand- display the surface for category ligand in all opened models
surface main #0- display the surface for category main in model 0 only
surface #1:5- display the surface for model 1, residue 5
~surface #1:5,32,64- undisplay surface for model 1, residues 5, 32 and 64
Known problem: when a category includes disjoint regions, the surface will be drawn for only one of these regions. Placing such regions in separate categories allows them to be surfaced independently.
See also: surfcolor, surfrepr, surftransparency, vdw, the surface attributes panel, the Actions menu