Crystal Contacts Crystal Contacts icon

The Crystal Contacts tool checks for clashes between copies of a structure when they are positioned according to symmetry information in the input coordinate file (PDB or mmCIF). This tool was created to validate symmetry information for virus capsid structures in the Protein Data Bank. See also: Unit Cell, Find Clashes/Contacts

There are several ways to start Crystal Contacts, a tool in the Higher-Order Structure category. It is also implemented as the command crystalcontacts.

The Molecule (presumably read from a file with symmetry information) should be chosen from the list of open molecule models. Clicking Show Contacts checks for atomic contacts within the specified Contact distance between copies. Atoms to exclude from the calculation (solvent, etc.) should be deleted beforehand.

Results are given in the Reply Log and shown schematically with balls representing copies of the structure and red cylinders representing close contacts:

The steps are described in more detail below; the symmetry information is described as for PDB files, but the corresponding information from an mmCIF file can also be used. The Create copies of contacting molecules option indicates whether to load the full atomic coordinates of any contacting copies when Show Contacts is pressed.

Information on the contacts is listed in the Reply Log:

Each line reports a pair of contacting NCS asymmetric units. 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.

Close dismisses the Crystal Contacts dialog. Help opens this manual page in a browser window.

UCSF Computer Graphics Laboratory / June 2016