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

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-10-01

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From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-10-01

Subject: Re: How to fix sidechain rotamers for Refmac?
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-10-01

It is hard to believe that REFMAC is being driven by rotamer
conformations - REFMAC weighting scheme gives a low priority to fitting
a preferred rotamer - quite rightly since the SD on rotamer angles is
high. The ideal is only "ideal" for a residue in a near vacuum - the
interactions with other nearby atoms often distort rotamers a lot.

So the question is more about why the positive /negative peaks are
persisting.
One possibility is that there are alternate conformations and the
occupancies you are assigning are too high.
Another that you have created an ideal rotamer using neighbouring water
sites as say the OE1 OE2 for a GLU, and actually the side chain IS in
the wrong place.. This is extremelyy easy to do I find!

When you are worried it is a good idea to set the occupancies of the
side chains and nearby HOH to 0.00 - leave them in the pdb file - then
do a few cycles of refinement and check the maps again.
Eleanor

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.stogios@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
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Jobs
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-10-01

Next message:
Subject: Re: MOLREP
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-10-01