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

Usage:
~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):

• probeRadius, where rad is the radius in Å of the “rolling sphere” used to define the surface. A radius of 1.4 Å is often used to approximate a water molecule. Increasing the probe radius decreases surface bumpiness.
• vertexDensity, where dens is the density of points in the surface. A higher density gives a smoother, more finely triangulated surface, but uses more memory.
• allComponents - whether to check for multiple disconnected parts of a surface (components) rather than assuming there is only one. Disjoint surfaces could be nested, like bubbles inside a protein, or enclose separate sets of atoms far apart in space.

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

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.

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

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.

Examples:

surface #0

surface

surface ligand

surface #1:5-38

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:

• using split to make each chain a separate model, then generating surfaces for the new models
• using surfcat to define custom surface categories, then surface to generate surfaces for these categories