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: [log in to unmask]
> 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 <[log in to unmask]
>> 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
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