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.
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
Results are given in the
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.
- 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
The Create copies of contacting molecules option indicates whether to
load the full atomic coordinates of any contacting copies when Show
Contacts is pressed.
- 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
and opened as a separate model.
Information on the contacts is listed in the
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