Hi all, Just writing an update, as I have had two people contact me asking if I had found a solution and if I could share. I would like to apologize first for not phrasing my question to describe the situation simply. I had several suggestions that Coot, and PISA could do it but actually can not. Eugene Krissinel rephrased the question brilliantly.
"What is required, however, is optimal superposition on one pair of chains (one from each dimer) but measuring RMSD on the other pair of chains from same dimers." The solution was given by Thomas Holder and can be done in Pymol: Use rms_cur based on a sequence alignment obtained with "align", try: # make sequence alignment object (optional: cycles=0) align A1B1 & chain B, A2B2 & chain B, object=aln, transform=0 # get current rms for this alignment rms_cur A1B1 & aln, A2B2 & aln, matchmaker=-1 This will give the RMSD for other pair of chains. Thanks Dan
