Chimera Commands Index

surface atom-spec

~surface atom-spec

The surface command displays solvent-excluded molecular surfaces. A solvent-excluded surface is composed of probe contact, toroidal, and reentrant surface, whereas a solvent-accessible surface is traced out by the probe center. The command ~surface undisplays the surfaces. Surface display can be controlled for individual atom patches.

Analytical surface areas are reported for both the solvent-excluded and solvent-accessible surfaces in the Reply Log. Totals are given along with the contributions from each component (disconnected part). The solvent-excluded and solvent-accessible areas per atom and residue are assigned as attributes named areaSES and areaSAS, respectively.

The surfaces are created with embedded software from the MSMS package, described in:

Reduced surface: an efficient way to compute molecular surfaces. Sanner MF, Olson AJ, Spehner JC. Biopolymers. 1996 Mar;38(3):305-20.
The probe radius and density of vertices used to compute a molecular surface can be adjusted with setattr, the molecular surface attributes panel, or the Selection Inspector, or set prior to surface creation in the New Surfaces preferences.

A molecule model 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.

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 display style of a surface (solid, mesh, or dot) can be controlled with surfrepr and its transparency adjusted with surftransparency.


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 #1:5-38
- display the surface for residues 5-38 in model 1

See also: color, surfcat, surfcolor, surfrepr, surftransparency, intersurf, setattr, vdw, measure buriedarea, preset, Write DMS