Re: [ccp4bb] refmac refinement and multiple conformations

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

Previous message:
Subject: refmac refinement and multiple conformations
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2007-03-16

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Subject: Can't choose full H-M symbol for conventional cell ?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-03-16

Subject: Re: refmac refinement and multiple conformations
From: Dirk Kostrewa dirk {- dot -} kostrewa {- at -} PSI {- dot -} CH
Date: 2007-03-16

Hi Li Yang,

REFMAC refines models with alternate conformations without any problems,
as long as the proper PDB syntax is used. Differences in R-factors might
stem from using different refinement programs that use different ways of
scaling (for example overall anisotropic vs. isotropic scale factor)
and/or different bulk solvent corrections (using a mask for protein vs.
double exponential scaling). In your case, the subset used for the
Free-R is presumably correct, otherwise you would use reflections from
the working set which should give lower values than the one reported ...

Best regards,

Dirk.

yang li wrote:
> If a pdb file contains some residues that have multiple conformations,
> when using refmac to refine it, will the programm take consider of
> these conformations? It seems that refmac would do this but I am not
> very sure. I downloaded a structure with some conformations from the
> pdb, but after refmac the R free is not as low as on the website. What
> is the problem? Thanks!
>
> Li Yang

--

****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: dirk.kostrewa@psi.ch
http://sb.web.psi.ch
****************************************

CCP4bb navigation

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

Previous message:
Subject: refmac refinement and multiple conformations
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2007-03-16

Next message:
Subject: Can't choose full H-M symbol for conventional cell ?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-03-16