Chimera2 logo

Command: surface

Usage:
surface  atom-spec1  [ enclose  atom-spec2 ] [ include  atom-spec3 ] [ replace true | false ] [ probeRadius rad ] [ gridSpacing s ] [ resolution r  [ level l ]] [ sharpBoundaries true | false ] [ visiblePatches N ]

Usage:
surface  atom-spec1  ( hide | show )
surface  atom-spec1  close
surface  surf-model  close

The surface command creates and displays molecular surfaces, either atomically detailed solvent-excluded surfaces (default) or lower-resolution Gaussian surfaces specified with the resolution option. A solvent-excluded surface (SES) is composed of the contact, toroidal, and reentrant surfaces of a probe sphere rolled over the spacefilling atoms. By contrast, a solvent-accessible surface (SAS, not shown by Chimera) is the surface traced out by the center of the probe sphere. See below for surface creation options and examples.

With atom-spec1, display can be controlled for entire molecular surfaces on down to individual atom or residue patches within a molecular surface; see the examples. By default, molecular surfaces are generated to enclose only the residues in biopolymer chains, grouped by chain ID. Typically, this gives a separate molecular surface for each peptide or nucleic acid chain. If only a subset of the atoms in a chain is specified, only the surface patches for those atoms in the context of the chain will be shown. The command surface with the hide keyword undisplays molecular surface patches for the specified atoms; the show keyword indicates displaying patches for the specified atoms in pre-existing surfaces only. The command surface with the close keyword removes all surface models that enclose any of the specified atoms, or removes the specified surf-model.

By default, each biopolymer chain in an atomic model will give rise to a separate surface model. Molecular surface models are treated as “children” of the corresponding atomic model. For example, surface models based on atoms in model #1 will be numbered #1.1, 1.2, etc., and closing #1 will also close those surface models. However, if a single surface model is based on atoms from more than one model (for example, generated with surf enclose #1,2), it will be assigned a number at the same level as the atomic models (for example, #3).

** The following categorization is not yet implemented; currently, the default surfaces simply include the biopolymer chains. **

Automatic Categories 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; by default, molecular surfaces enclose these, grouped by chain ID

Surface Creation Options

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.

Grouping Atoms into Surfaces

The enclose option can be used to specify a different set of atoms (atom-spec2) to enclose within a single surface, for example, to coalesce biopolymer chains with different chain IDs into a single molecular envelope.

The include option can be used to force including atoms that would otherwise be ignored (residues not within a biopolymer chain, such as ligands, solvent, and ions) into the same envelope as the biopolymer atoms with the same chain ID. For convenience, however, if atom-spec1 contains only such atoms, they will be surfaced separately and the include option is not needed.

The replace option (default true) indicates removing all previously created surface models that enclose any of the same atoms as the current surface. Successive uses of the surface command with replace false can produce multiple surface models that enclose the same set of atoms or different but overlapping sets of atoms. Surface model number assignments are discussed above.

Calculation Parameters

Aside from how atoms are grouped, molecular surface parameters can be specified with the following options:

Other Appearance Options

The sharpBoundaries option (default true for an SES, default false for a Gaussian surface) adjusts the triangulation of the surface to produce abrupt and relatively straight boundaries between per-atom patches. This significantly reduces the sawtooth appearance where adjacent per-atom patches differ in color or display status (hidden vs. shown).

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.

Examples

Example surface commands:

surface
- display the surface of each biopolymer chain in each model
surface #1
- display the surface of each biopolymer chain in model 1
surface #1:5-38
- display the surface patch(es) for residues 5-38 in each chain of model 1
surface #1/A:5-38 hide
- hide the surface patch(es) for residues 5-38 in chain A of model 1
surface :10-20 visible 1
- display the largest surface patch for residues 10-20 in each chain
surface /b close
- close (delete) the surface model for chain B
surface #1.2 close
- close (delete) the surface with model number 1.2
surface #1-3
- display the surface of each biopolymer chain in models 1-3
surface #1-3 enclose #1-3
- display a single surface enclosing all biopolymer chains in models 1-3; the first #1-3 could be omitted, as a blank specification there is interpreted as “all”
surface :10-20 enclose /a-c
- display the surface patch(es) for residues 10-20 within a single surface that encloses chains A-C
surface #1 include :hem
- display a surface that encloses each biopolymer chain in model 1 along with its respective HEM residue (for example, in PDB 4HHB)
surface enclose #1 include :hem
- display a single surface that encloses all the biopolymer chains and HEM residues in model 1

Technical Notes

Patch boundaries. Per-atom surface patch boundaries are defined by associating each surface point with an atom. In a solvent-excluded surface, each point is associated with the atom with the smallest distance normalized by radius (the atom with the smallest d/r, where d is the distance between the surface point and the atom center, and r is the atomic VDW radius). In a Gaussian surface, each point is simply associated with the closest atomic center.


UCSF Resource for Biocomputing, Visualization, and Informatics / August 2015