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, or set prior to surface creation in the New Surfaces preferences.
A molecular structure is automatically divided into the following mutually exclusive categories:
| Automatic 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 |
| solvent |
of the following two, the set with the greater number of residues:
|
| ligand | single residues or bonded sequences of residues with < 10 residues per bonded sequence, < 250 atoms, and < 1/4 the number of atoms in the largest bonded sequence of residues in the model |
| main | all remaining atoms |
Each category name can be used in atom-spec strings. The surface will be calculated for each entire category that contains any specified atoms, but only the surface corresponding to those atoms will be displayed. Using surface with a blank atom-spec displays the surface for all atoms in category main.
The command ~surface undisplays surfaces, and when used with a blank atom-spec, undisplays the surface for all atoms in all categories.
Categories can be defined manually with surfcat 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.
The surface representation (solid, mesh, or dot) can be controlled with surfrepr. Surface display and style can also be controlled with the Actions menu and the surface attributes panel.
Examples:
surface #0- display the surface for all categories in model 0
surface- display the surface for category main in all models
surface ligand- display the surface for category ligand in all 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
See also: surfcat, surfcolor, surfrepr, surftransparency, vdw, preset