Intersurf is the command-line implementation of the Intersurf tool, which creates and displays interface surfaces. Intersurf with atom specification arguments generates an interface surface. Intersurf color (not yet implemented) defines a color mapping to be used for subsequently created interface surfaces. Currently, the distance-to-color mapping can only be adjusted with the graphical user interface (see below).
An interface surface is opened as a separate model that can be:
intersurf #0:.a #1:.b pair chain prune 15 bias .2- generate an interface surface between chain A in model 0 and chain B in model 1, biasing the surface toward the former; disregard residues in each chain whose centroids are not within 15.0 Å of any residue centroid in the other chain
intersurf main ligand pair atom solid false- generate a mesh interface surface between the sets of atoms classified as main and ligand
The option keywords apply only to interface surface generation, not coloring. Option keywords for intersurf can be truncated to unique strings and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.
pairing model|chain|atomIt is necessary to use pairing chain to specify an interface between chains in two different models and pairing atom to specify an interface between sets of atoms (other than whole chains or whole models) in two different models.
- model - calculate an interface surface between two models; default when atom-spec1 and atom-spec2 specify atoms in two different models
- chain - calculate an interface surface between two chains; default when atom-spec1 and atom-spec2 specify atoms in the same model (of course, they should specify two different chains)
- atom - calculate an interface surface between two sets of atoms that are not whole chains or models (atom-spec1 and atom-spec2 should specify mutually exclusive sets of atoms); this can only be done with the command intersurf, not the Intersurf graphical interface
bias fraction
How to divide the space between the two sets of atoms. Each point in an interface surface separates and specifically corresponds to two atoms, one from each set. The fraction can range from 0 to 1, where 0.5 (default) places each surface point equidistant from the two corresponding atoms. Values < 0.5 place the surface closer to the set specified with atom-spec1 and values > 0.5 place the surface closer to the set specified with atom-spec2.
prune distance
Ignore residues in one set of atoms whose centroids are not within distance (default 30.0 Å) of any residue centroid in the other set of atoms. If this option is not specified, or if distance is set to 0.0 Å, pruning will not be performed.
solid true|false
Whether to generate a solid surface rather than the default mesh.
track true|false
Whether to overwrite any existing interface surface (otherwise, an additional surface model will be generated).
See also: Color Zone, Surface Color, Surface Zone, Measure Volume