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: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-10-02

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Subject: Re: How to fix sidechain rotamers for Refmac?
From: iulek {- at -} INTERPONTA {- dot -} COM {- dot -} BR iulek {- at -} INTERPONTA {- dot -} COM {- dot -} BR
Date: 2009-10-02

Besides possibilities pointed, I would ask if your are using undue NCS
restraints, id est, between "rotamers" which are genuinely "different".
Anyway, at 1.8 A resolution, one should check the adequateness of using
NCS restraints.

J
> 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: Saint into Scala
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-10-02

Next message:
Subject: gpp4 version 1.2 released
From: Morten Kjeldgaard mok {- at -} BIOXRAY {- dot -} AU {- dot -} DK
Date: 2009-10-02