Hi Joe,
Thanks so much Pavel for the very rapid response! One more thing, it is a disulfide linked DTT so do I do anything special to ensure that all the sulfur atoms (4 in total - two in one unit cell - one each from the cys and dtt and two in the other unit cell) stay in close enough contact for a covalent bond and not move due to non-bonded contact distance restraints?
phenix.refine shows a summary of the disulfides like this: Number of disulfides: simple=1, symmetry=1 Simple disulfide: pdb=" SG CYS A 2 " - pdb=" SG CYS A 14 " distance=2.09 Symmetry disulfide: pdb=" SG BCYS A 133 " - pdb=" SG BCYS A 133 " distance=2.12 -x,y,-z The program should find all disulfides automatically, using the disulfide_distance_cutoff=3 parameter. Let us know if the output doesn't look right. Ralf