The gather command will take a full model (e.g. one that contains a separate occurrence of each molecule in the asymmetric unit) and average it over the noncrystallographic symmetry to produce a coordinate file with only the unique parts of the asymmetric unit represented. For example, assume we have a model with four identical chains (named O, A, B, and C) in the asymmetric unit and the noncrystallographic symmetry cluster CRO is defined to cover all residues of each chain. After the gather command the new coordinate file will contain one chain, named CRO, which is the average of all four chains. In addition to the new coordinate file, gather will write out a small file which contains the TRANSFORMATION statements which describe the rotation and translation required to overlay each chain on the prototype.
The files written by the gather command are gathered.cor
and
gathered.ncs.