[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [ccp4bb]: Conclusion of bulk solvent corrected fo-fc map (B-factor restraints)



***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

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:
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> 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
****************************************