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 8 Mar 2010, at 22:11, Jim Fairman wrote:
I have a similar situation so I am also curious for the answer.
Refmac will always try to form a disulfide bond with both conformers
for me as well.
On Mon, Mar 8, 2010 at 4:55 PM, Critton, David <[email protected]
> 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
--
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9229
E-mail: [email protected] [email protected]
