Crystal Contacts

The Crystal Contacts tool checks for clashes between copies of a structure when they are positioned according to symmetry information in the header of the PDB file. Each copy of the original structure is shown as a ball, and close contacts between copies are shown as cylinders connecting the balls. 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 PDB file with symmetry information) should be chosen from the list of open molecule models. When Show Contacts is clicked, Crystal Contacts generates a unit cell outline box and balls representing the symmetry copies of the structure. Cylinders are drawn between pairs of copies within the Contact distance of each other.

More specifically, Crystal Contacts:

• uses CRYST1 information to draw a unit cell box with one corner at (0,0,0).
  
  
• represents the structure in the PDB file as a single green ball, even if it includes multiple chains.
  
  
• uses MTRIX records to generate copies related by noncrystallographic symmetry, also shown in green; the green balls collectively represent one crystal asymmetric unit (CAU). If there are no MTRIX records, the starting structure is already the CAU and only one green ball will be shown (example: 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: 1v9u). Each ball represents a single NCS asymmetric unit.
  
  
• uses CRYST1 or SMTRY records to generate copies related by crystallographic symmetry, shown in blue; the blue and green balls together represent the contents of one crystal unit cell.
  
  
• identifies copies with any atom within the Contact distance of a copy shown in green. A red cylinder with radius proportional to the number of contacting atoms is drawn to represent the contact; the minimum and maximum cylinder radii are limited, with the minimum corresponding to 1% of atoms in contact and maximum corresponding to 5%. Copies in neighboring unit cells are shown as yellow balls if any of them form close contacts with a copy shown in green. Copies right on top of each other are shown with a transparent green ball rather than a connecting cylinder.
  
  
• lists information on the contacts 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.