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From: Peter J Stogios <[log in to unmask]>
To: [log in to unmask]
Sent: Wednesday, September 30, 2009 12:22:54 PM
Subject: [ccp4bb] How to fix sidechain rotamers for Refmac?

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: [log in to unmask]
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