Chimera Commands Index

crystalcontacts  model_number  distance  options

The crystalcontacts command checks for clashes between copies of a structure when they are positioned according to symmetry information in the input coordinate file (PDB or mmCIF). It is the command-line implementation of Crystal Contacts.

The structure must have been opened from a file containing symmetry information; otherwise, there is no reason to use this command. The model_number (preceded by #) specifies the structure, and distance specifies what will be considered a close contact. Atoms to exclude from the calculation (solvent, etc.) should be deleted beforehand.

By default, the results are reported in the Reply Log and shown schematically with a marker set in which balls represent copies of the structure and red cylinders represent close contacts:

See Crystal Contacts for details. See also: sym, distance, findclash, Unit Cell


Option keywords 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.

copies true | false
Whether to load the full atomic coordinates of any contacting copies.
residueInfo true | false
Whether to write a table of residue contact information to the Reply Log.
buriedAreas true | false
Whether to calculate per-residue buried solvent-accessible surface area (SASA) values and report them in the Reply Log. To calculate the buried area for a given residue, only the residues in contact with that residue are used; this procedure is computationally much more tractable but may give slightly different results than a buried-area calculation using all atoms in multiple copies of the structure. Thus, the distance used to define contacts should be large enough to include all atoms with buried SASA, at least twice the probe radius plus twice the maximum VDW radius (with default radii, about 6.6 Å). Each contacting residue will be assigned an attribute named maxCrystalBuriedArea that gives the maximum buried SASA of any of its copies within the crystal.
probeRadius  r
The probe radius r (default 1.4 Å) is the size of the sphere rolled over the surface for buried area calculations.
intraBioUnit true | false
Whether contacts between subunits in the same biological unit should be included in the results. The biological unit is defined by BIOMT matrices in the input PDB file.
schematic true | false
Whether to show the results schematically with balls and cylinders (whether to create a marker set).
replace true | false
Whether to replace any pre-existing marker set from crystalcontacts with the new one rather than generating an additional model.