Chimera Commands Index

intersurf atom-spec1 atom-spec2 options

Intersurf is the command-line implementation of the Intersurf tool, which creates and displays an interface surface between two specified sets of atoms.

The surface is generated as a surface model and assigned the same model number and transformation as the corresponding molecule model (or, if atoms from more than one model were used, the lowest-numbered of those models). Models can be hidden or closed using the Model Panel.

The surface is colored to show the separation across the interface, by default red for smaller distances and blue for larger. Currently this distance-to-color mapping can only be adjusted in the Intersurf graphical interface. However, alternative color mappings not based on the separation across the interface can be applied with scolor, or the surface can be colored to match nearby atoms using Color Zone. After an interface surface has been generated, the Intersurf graphical interface will contain a histogram populated with the corresponding atom-atom distances. A new color mapping can be defined in the histogram, then applied by reissuing the same intersurf command.


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|atom It 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.
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).
select true|false
Whether to select the atoms that define the interface.
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.
bias fraction
How to divide the space between the two sets of atoms. Each vertex in the interface surface lies between two atoms, one from each set. The fraction can range from 0 to 1, where 0.5 (default) places each interface surface point equidistant from the VDW surfaces of the two corresponding atoms. A value of 0.0 places interface surface vertices at the VDW surface of the set specified with atom-spec1 and a value of 1.0 places them at the VDW surface of the set specified with atom-spec2. Where the VDW surfaces of the two sets coincide, changes in the value will have little effect on interface surface vertex placement.

See also: scolor, measure buriedarea, Color Zone, Surface Zone, Measure Volume