Pavel, I sent you the associated pdb file as an attachment. The site in question is 169 in both monomer A and monomer B. I think one way around the problem for me is to create alternative conformations for the residues on either end of the modified cysteine. In that way I can refine each as a section of alternative conformations and then I think things should link up both in Phenix and COOT. COOT is particularly problematic. It only recognizes conformer A and not any additional conformers for a particular position if the name of the amino acid changes. I guess my case is not that common - ie a mixture of oxidation states of a regular amino acid. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________