Re: [ccp4bb] How to fix sidechain rotamers for Refmac?

[Roger Rowlett]

Is it possible there are alternate conformations for these side chains? Refmac, or any other refinement program, will try to fill one of the density regions with your side chain, but because of partial occupancy, a negative difference map will result, with accompanying positive density in the other rotamer position. To sort this out without bias, do an "omit" map of the side chain by mutating it to Ala for one round of refinement. That should show you the effective side chain electron density Refmac is trying to fit. Cheers. 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 -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu