The crystalcontacts command checks for clashes between copies of a structure when they are positioned according to symmetry information in the header of the PDB file. It is the command-line implementation of Crystal Contacts.
The structure must have been opened from a PDB file containing symmetry information; otherwise, there is no reason to use this command. The model_number (optionally preceded by #) specifies the structure, and distance specifies what will be considered a close contact.
Crystalcontacts draws a unit cell box with one corner at (0,0,0) and represents the starting structure and each additional copy with a ball. The set of one or more green balls comprises the crystal asymmetric unit, the blue and green balls together represent the contents of one crystal unit cell, and any yellow balls represent copies in neighboring unit cells. Close contacts involving any green copies are detected and indicated with red cylinders. Cylinder radius varies, with the thinnest cylinders representing close contacts of 1% or fewer of the atoms in a copy and the fattest representing close contacts of 5% or more of the atoms. Information on the contacting pairs of copies is written to the Reply Log.
Consult the Crystal Contacts manual page for further details.