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.
The Crystal Contacts tool
can be opened from the Higher-Order Structure section of the
Tools menu and manipulated like other panels
It is also implemented as the command
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.
- Create copies of contacting structures
– load contacting copies as full atomic models
- Rainbow color copies
– whether to rainbow-color the additional atomic models;
otherwise, they will be the same color as the original
- Show schematic of contacting structures
– generate a schematic representation
of the copies and contacts
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
[back to top: Crystal Contacts]
How Copies are Generated
- CRYST1 information is used to define a unit cell box
with one corner at (0,0,0).
- 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).
- 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.
[back to top: Crystal Contacts]
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.
- light green balls – the original structure and
any copies related by noncrystallographic symmetry, collectively
representing the crystallographic asymmetric unit (CAU)
- light blue balls – copies related by crystallographic symmetry,
together with the green balls representing the contents of one unit cell
- light red cylinders – close contacts between copies, with radii
proportional to the number of contacting atoms.
the minimum and maximum cylinder radii are limited, with the minimum
corresponding to 1% of atoms in contact and maximum corresponding to 5%.
- yellow balls – any copies from neighboring unit cells found
to be within the contact distance of any copy in the CAU
- light blue cylinders – outline of a unit cell box, where
the contents of a unit cell could be placed relative to each vertex
- copies right on top of each other are shown with a transparent green ball
rather than a connecting cylinder
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
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