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Re: [ccp4bb]: Conclusion of bulk solvent corrected fo-fc map (B-factor restraints)
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I use the following weights which result from a molecular dynamics simulation
by Yu & Karplus (1985), Acta Cryst. B41, 191-201 in the old PROLSQ days.
They've checked how sensible the default B-factor restraints (1.0,1.5,1.5,
2.0) were and came basically to the conclusion that they should be lowered by
a factor of ~2 for main chain and a factor of ~3 for side chain restraints.
>From then on I'm using the following restraints with good experience:
Main chain bond 2.0 A**2
Main chain angle 3.0 A**2
Side chain bond 4.5 A**2
Side chain angle 6.0 A**2
A probably better approach are the side chain specific B-factor restraints
used in the later versions of TNT based on the observed B-factor distribution
in high resolution protein cystal structures by Tronrud (1996), J. Appl.
Cryst., 29, 100-104.
Best regards,
Dirk.
On Thursday 13 March 2003 23:04, Mark DePristo wrote:
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>
> The default values (for refmac5.1.24) are:
>
> THERMAL FACTORS
> Weight= 1.00
> Main chain bond (1-2 neighbour) 1.50A**2
> Main chain angle (1-3 neighbour) 2.00A**2
> Side chain bond 3.00A**2
> Side chain angle 4.50A**2
>
> The looser parameter set is enabled by:
>
> BFAC 1 5 6 6 7.5
>
> which produces:
>
> THERMAL FACTORS
> Weight= 1.00
> Main chain bond (1-2 neighbour) 5.00A**2
> Main chain angle (1-3 neighbour) 6.00A**2
> Side chain bond 6.00A**2
> Side chain angle 7.50A**2
>
> Mark
>
> On Thursday, March 13, 2003, at 01:44 PM, wgscott@chemistry.ucsc.edu
>
> wrote:
> > Please let us know what weightings you are now using.
> >
> >> One definite conclusion (thanks to Ian Tickle) is that the default
> >> B-factor restraints in refmac are definitely too tight (and incorrect
> >> in the HTML documentation). Loosening them up ...
>
> Mark DePristo
> Ph.D. Candidate
> Dept. of Biochemistry
> Cambridge University
> mdepristo@cryst.bioc.cam.ac.uk
> http://www-cryst.bioc.cam.ac.uk/~mdepristo/
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OSRA/007
CH-5232 Villigen PSI, Switzerland
E-mail: dirk.kostrewa@psi.ch
Phone: +41-56-310-4722
Fax: +41-56-310-4556
WWW: http://www.sb.psi.ch
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