Crystal Contacts

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:

• light green balls - the original structure and any copies related by noncrystallographic symmetry
• light blue balls - copies related by crystallographic symmetry, together with the green balls representing the contents of one unit cell
• yellow balls - copies from neighboring unit cells
• light red cylinders - close contacts between copies, with thicker cylinders indicating greater numbers of contacts
• light blue cylinders - outline of a unit cell box, where the contents of a unit cell could be placed relative to each vertex

• CRYST1 information is used to draw a unit cell box with one corner at (0,0,0).
  
  
• The structure in the PDB file is represented as a single green ball, even if it includes multiple chains.
  
  
• MTRIX records are used 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: 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). Each ball represents a single NCS asymmetric unit.
  
  
• CRYST1 or SMTRY records are used to generate copies related by crystallographic symmetry, shown in blue; the blue and green balls together represent the contents of one crystal unit cell.
  
  
• Copies with any atom within the Contact distance of a copy shown in green are identified. 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.
  
  
• The balls and box are created as a marker set and opened as a separate model.

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.