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The SSBOND record does not allow the specification of an "alternate location indicator". The PDB practice is to list the SSBOND record if any confirmation is in an SS-bond. I think that refmac has problems with this since it will try to apply the SSBOND patch to both confirmations. The workaround is to use the LINK record in refmac for the SS-bonded A confirmation (which allows alternate atoms to be specified) and use a link_id of SS. Refmac should then generate the correct restraints for the conformer involved in the disulfide bond. Note that this should probably be listed as SSBOND in the header for the deposited PDB file. Regards, Mitch See http://www.wwpdb.org/documentation/format23/sect6.html http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_ssbond -----Original Message----- From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Prasenjit Bhaumik Sent: Friday, July 06, 2007 10:46 AM To: [log in to unmask] Subject: [ccp4bb] Double conformations of cysteine ! Hello, We are trying to refine a structure using REFMAC and we are facing problem in refining the double conformations of a cysteine residue. One conformation is involved in formation of a disulfide linkage and other conformation is free. Is there any way to define the restraints so that both the conformations can be refined. With kind regards, Prasenjit -- Prasenjit Bhaumik, Ph.D. Protein Structure Section Macromolecular Crystallography Laboratory National Cancer Institute at Frederick 1050 Boyles Street, Building-539, Room-145 P.O. Box B, Frederick, MD-21702, USA Phone: 301-846-1974, Fax: 301-846-7101 E-mail: [log in to unmask] -------------------------------------------------