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Tool: Crystal Contacts

Crystal Contacts checks for close contacts between symmetry-related copies of an atomic structure. The symmetry information is read from the input coordinate file (PDB or mmCIF). Descriptions below are for PDB symmetry records, but the equivalent information from mmCIF is used in the same way. See also: Unit Cell, Clashes/Contacts, Select Contacts, Distances, interfaces, sym

The Crystal Contacts tool can be opened from the Higher-Order Structure section of the Tools menu and manipulated like other panels (more...). It is also implemented as the command crystalcontacts.

The Atomic structure of interest should be chosen from the list of current atomic models, and the desired contact distance specified (default 3.0 Å).

Clicking Options shows/hides additional options:

Clicking Show Contacts generates copies, identifies atomic contacts within the specified contact distance, and shows them according to the options. Any atoms one wishes to exclude from the calculation (solvent, etc.) should be deleted beforehand. Clicking Delete Contacts removes the atomic copies and/or schematic representation. Clicking Help shows this page in the Help Viewer.

Crystal contact information is listed in the Log. Each line reports a pair of copies (NCS asymmetric units) that are in within the specified distance of one another. While low numbers of contacting Atoms are fairly common, very high numbers (especially complete overlap of the structures) indicate there may be an error in the symmetry information. An index MTRIXref tells which MTRIX record positions one subunit, and indices MTRIX, SMTRY, and Unit cell identify the other. The MTRIX and SMTRY matrix indices start at 0, and therefore do not exactly match the matrix numbers given in the PDB header.

Each unique relative orientation of contacting NCS asymmetric units is reported, and the number of occurrences of geometrically equivalent pairs with the same contacts is given in the Copies column of the table. Because of round-off errors in computing symmetry matrices, tolerances of 0.1 degrees and 0.1 Å are used to identify equivalent relative orientations.

Detailed information on the interacting residue pairs can be reported using the crystalcontacts command with residueInfo true.

How Copies are Generated

  1. CRYST1 information is used to define a unit cell box with one corner at (0,0,0).
  2. MTRIX records are used to generate copies related by noncrystallographic symmetry. Together with the original, these copies make up the crystal asymmetric unit (CAU). If there are no MTRIX records, the starting structure is already the CAU (example: PDB entry 1bzm). Icosahedral capsid structures typically contain a fraction of the CAU, a noncrystallographic symmetry (NCS) asymmetric unit that must be duplicated according to MTRIX records to generate the CAU (example: PDB entry 1v9u).
  3. CRYST1 or SMTRY records are used to generate copies related by crystallographic symmetry. Together with the copies from the previous step, these copies make up one crystal unit cell.

Schematic Representation

In the schematic, balls represent copies of the atomic model and red cylinders represent close contacts. The original atomic model (and each of its copies) is represented by a single ball, even if it includes multiple chains.

The balls may not be packed into the unit cell box because the matrices in the input file are only required to generate the correct symmetries, not to pack the resulting copies within the box.

The balls and cylinders are created as a marker set.

UCSF Resource for Biocomputing, Visualization, and Informatics / May 2022