Surface selectively displays molecular surfaces. Although nominally a "standard Midas command," surface has undergone substantial changes:
M.F. Sanner, A.J. Olson, and J.C. Spehner, "Reduced surface: an efficient way to compute molecular surfaces" Biopolymers 38:305 (1996).The surface calculated in Chimera consists of probe contact plus reentrant surface; this is different from the surface traced out by the probe center (often called the solvent-accessible surface). The probe radius and density of vertices used to compute the surface can be viewed and changed using the surface attributes panel.
When a model is read in, it is automatically divided into the following mutually exclusive categories:
| Automatic Categories | |
|---|---|
| category-name | definition |
| ions | singleton atoms of atomic number 9 or greater |
| solvent |
singleton atoms of atomic number 8 or less and
non-ion single residues that satisfy all of the following:
|
| ligand | non-solvent, non-ion single residues or bonded sequences of residues no more than 1/4 the size (in terms of number of atoms) of 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).
Examples:
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, msms, vdw, the surface attributes panel, the Actions menu