Thank you for the prompt replies! I was able to resolve the issue by specifying an 'SS' id in the 'LINK' record for the individual conformers. (see Garib's post below)
> From: CCP4 bulletin board on behalf of Garib Murshudov > Sent: Mon 3/8/2010 5:21 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Multiple conformations of disulfide-linked cysteines > > Automatically yes. But you can force it to use only one conformation. > You need to use link record instead of ssbond (they are essentially > same). To do this you need to put link records just before cryst1 > card. Examples of link record are in: > > http://www.ysbl.york.ac.uk/refmac/data/template_link.txt > > For ssbond only on a specified alt conf. you need something like: > > LINK SG ACYS B 1 SG ACYS B > 22 SS > > Please make sure that item names in the link line is positioned > correctly. PDB is extremely position sensitive > Garib > > >> On Mon, Mar 8, 2010 at 4:55 PM, Critton, David <david_crit...@brown.edu >> wrote: >> 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
