Hi Peter,
sorry for not answering exactly your question... but since this is
relevant I reply anyway:
The latest version of phenix.refine has an option "fix_rotamers=true",
that automatically fixes all side chain rotamers by going
residue-by-residue and choosing the best one based on density fit and
Molprobity rotamer library.
The algorithmic details are here:
http://cci.lbl.gov/~afonine/fix_rotamers/fit_rotamers.pdf
Please note that this is a development version and the corresponding
code is 3 days old -:) More details will be published soon.
Please let me know if you have questions.
Pavel.
On 9/30/09 9:22 AM, Peter J Stogios wrote:
Hi,
I'm working with a 1.8 A structure with Coot and Refmac, and there are
many sidechain rotamers that show very clear difference density peaks
for setting their correct positions. However, Refmac continuously
moves the rotamers back into negative density peaks. It's really
quite silly because often there is an obvious positive density peak
near to a negative density peak.
I have tried using automatic geometry weighting and manually setting
the weighting term to a very tight 0.025, but each has no effect. I
have also tried increasing the torsion angle restraint term to 2.0 but
this also has no effect.
Does anyone have any suggestions? Is there any way to "fix" atom
positions for Refmac?
Thanks in advance,
~
Peter J Stogios, Ph.D.
Postdoctoral Research Fellow
e: p.stog...@utoronto.ca
p: 416-978-4033
w: http://www.uhnres.utoronto.ca/centres/proteomics/
Structural Proteomics in Toronto Research Group, University Health
Network
C.H. Best Institute
112 College Street, Room 70
Toronto, Ontario, Canada M5G 1L6
