Chimera Commands Index

surface atom-spec

~surface atom-spec

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 molecular 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:
  • "small solvent" candidate set: singleton atoms in residues named WAT, HOH, and DOD, plus singleton atoms of atomic number 6-8 in single-atom residues
  • "other solvent" candidate set: excluding residues in the "small solvent" set, the most prevalent type of residue that is not covalently bonded to other residues, has ≤ 10 atoms per residue, and is present in at least 10 copies in the structure
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 molecular surface attributes panel.


surface #0
- display the surface for all categories in model 0
- 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