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: [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
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