Addition of symmetry-related contact restraints to PROTIN and PROLSQ

Abstract

Symmetry-related van der Waals contacts and hydrogen bonds are stereochemical restraints which are often ignored in macromolecular structure refinement programs. PROTIN and PROLSQ have been modified to account for symmetry-related contacts. The derivatives calculated for an atom in its symmetry-transformed position need only be multiplied by the appropriate rotation matrix to be applied to the atom in its untransformed position. Therefore the code already present in PROLSQ for van der Waals contacts is readily adapted to account for symmetry-related contacts. The `cubing' algorithm, shown to be much faster than residue-by-residue center and radius methods for generating potential contacts, has been incorporated in PROTIN.