The SSBOND record format cannot take alternate id's. However, refmac allows using LINK records (or LINKR in the newer versions) which support alternate id designations with the link id set to "SS" to refine disulfide bonds with alternates. See http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_ssbond
Regards, Mitch P.S. At deposition time, the PDB annotator will remove the LINK records and replace them with SSBOND records. However, they will only generate connect records for the alternate groups which are close enough to bond, not both alt ids. -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Critton, David Sent: Monday, March 08, 2010 1:55 PM To: [email protected] Subject: [ccp4bb] Multiple conformations of disulfide-linked cysteines Dear CCP4BB, I am building a protein structure containing a pair of cysteines linked via disulfide bond. This disulfide bond (i.e. the cysteine S-gamma atoms) refines well at 2/3 occupancy, however the electron density suggests that these cysteines each adopt a second, unlinked conformation (presumably at 1/3 occupancy). I have no trouble building the alternate conformers; however, refinement causes both conformers to disulfide-bond. I would like to know if there is a way (and how) to specify individual conformers (or individual atoms) in the SSBOND record of a PDB. Thank you in advance, David A. Critton Graduate Student, Page Laboratory Department of Molecular Biology, Cell Biology & Biochemistry Brown University Providence, RI
