Chimera Commands Index

surface [ probeRadius rad ] [ vertexDensity dens ] [ allComponents true | false ] [ visiblePatches N ] [ warnLarge true | false ]  atom-spec

~surface atom-spec

The surface command calculates and 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. See also: color, scolor, surfcat, surfcolor, surfrepr, transparency, intersurf, setattr, vdw, preset, Write DMS, surface calculation failures and workarounds

Option keywords for surface can be truncated to unique strings and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0.

Molecular surface parameters can be specified with the following options (defaults are in the New Surfaces preferences):

After surface creation, these parameters can also be adjusted with setattr, the molecular surface attributes panel, or the Selection Inspector.

The visiblePatches option indicates hiding all but the N largest connected surface patches (per surface model) for the specified atoms; by removing the visual clutter of small patches, this can significantly enhance viewing of pocket surfaces. Ranking to determine the largest is based on surface area, including any portions hidden by clipping. See also: sop zone

Using warnLarge false suppresses the confirmation dialog that would otherwise appear before the calculation of a large number of surfaces (default warnLarge true).

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). Totals are for entire surfaces even if they are only partially displayed; however, the solvent-excluded and solvent-accessible areas per atom and residue are assigned as attributes named areaSES and areaSAS, respectively, and sums over specified sets can be obtained with the Attribute Calculator tool. Calculating relative exposure (a normalized surface area) may be helpful for classifying amino acid residues as buried or exposed. See also: measure, CASTp Data, Area/Volume from Web, Measure and Color Blobs

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.
MSMS surface calculations may fail numerically, especially on large structures; see surface calculation failures and workarounds.

A molecule model is automatically divided into the following mutually exclusive categories:

Automatic Categories
name membership rules, in order of application
solvent of the following two, the set with the greater number of residues:
  • “small solvent” candidate set: residues of up to 3 atoms named WAT, HOH, and DOD, plus singleton atoms (i.e., not covalently bonded to other 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
ions non-solvent singleton atoms other than noble gases, plus covalently bonded groups of ≤ 4 atoms (not counting hydrogens) in the same residues as those singletons
ligand singleton atoms that are noble gases; 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; residues bonded to a chain but not included in its main sequence (e.g., retinal in rhodopsin, glycosylations)
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.


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

Categories can be defined manually with surfcat when the automatic categories do not give the desired results. By default, protein and nucleic acid chains are classified as main, and if multiple chains are in contact, they will be enclosed in a single surface. If separate surfaces for the separate chains are preferred, approaches include: