ChimeraX docs icon

Command: crystalcontacts

crystalcontacts  atomic-model  [ distance  r ] [ copies  true | false ] [ rainbow  true | false ] [ schematic  true | false ] [ intraBiounit  true | false ] [ residueInfo  true | false ] [ buriedAreas  true | false ] [ probeRadius  r ]

crystalcontacts delete  atomic-model 

The crystalcontacts command checks for close contacts between symmetry-related copies of atomic structures. It is the command-line implementation of the Crystal Contacts tool. The symmetry information is read from the input coordinate file (PDB or mmCIF). See also: unitcell, clashes/contacts, interfaces, sym

One or more atomic models can be specified. Any atoms one wishes to exclude from the calculation (solvent, etc.) should be deleted beforehand. Symmetry copies can be shown as full atomic models and/or represented schematically. Results are reported in the Log (details...).


distance  d
The distance d (default 3.0 Å) defines what is considered an atomic contact between copies.
copies  true | false
Whether to load the full atomic coordinates of any contacting copies (default true). Any previous set of contacting copies for the structure will be replaced automatically with the new copies.
rainbow  true | false
Whether to color the additional atomic copies sequentially using the rainbow palette:
(default true). If the option is false, the copies will be colored in the same way as the original structure.
schematic  true | false
Whether to show a schematic representation of the results (default false): unit cell outline, copies shown as balls, and contacts shown as red cylinders, with thicker cylinders indicating greater numbers of contacts. The schematic is generated as a marker set. Any previous schematic for the structure will be replaced automatically with the new one.
intraBiounit  true | false
Whether contacts between subunits in the same biological unit should be included in the results (default true). The biological unit is defined by BIOMT matrices in the input PDB file.
residueInfo  true | false
Whether to write a table of residue-residue contact information to the Log (default false). Each line reports a contact between residues in different copies (NCS asymmetric units) and their closest interatomic distance. Several columns identify the specific residues and the copies in which they reside (symmetry operator, ncs operator, and unit cell of the second residue relative to the original copy).
buriedAreas  true | false
Whether to calculate per-residue buried solvent-accessible surface area (SASA) values and report them in the Log (default false). To calculate the buried area for a given residue, only the residues in contact with it according to the specified distance are used; this procedure is faster but may give slightly different results than a buried-area calculation using all atoms in multiple copies of the structure. To give very similar results, the distance 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).
probeRadius  r
The probe radius r (default 1.4 Å) is the size of the sphere rolled over the surface for buried area calculations.

UCSF Resource for Biocomputing, Visualization, and Informatics / March 2021