[ccp4bb] How to fix sidechain rotamers for Refmac?

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

Previous message:
Subject: Phaser question
From: Simon Kolstoe s {- dot -} kolstoe {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2009-09-30

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Subject: Re: How to fix sidechain rotamers for Refmac?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-09-30

Subject: How to fix sidechain rotamers for Refmac?
From: Peter J Stogios p {- dot -} stogios {- at -} UTORONTO {- dot -} CA
Date: 2009-09-30

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: Phaser question
From: Simon Kolstoe s {- dot -} kolstoe {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2009-09-30

Next message:
Subject: Re: How to fix sidechain rotamers for Refmac?
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-09-30