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):
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, 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:
|name||membership rules, in order of application|
of the following two, the set with the greater number of residues:
|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
surface- 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: