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Re: [ccp4bb]: B-factor and resolution
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Dear Gerard,
could you please repeat your
B-value (Debye Waller factor) analysis again
with structures determined from data better than
,say, 1.7 A. I believe that B-values are kind of
fudge factors at resolution lower than maybe
2.5 A, whereas at higher resolution they indeed
make sense, since the restraints are pratically
downweighted by the x-ray term.
Marius
_____________________________________________________________________________
Dr. Marius Schmidt
office:
The University of Chicago
Biochemistry and Molecular Biology
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On Thu, 4 Jan 2001, Gerard "CD" Kleywegt wrote:
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>
>
> well, i had a quick look at the data stored in QDB
> (gjk, acta cryst d52, 842-857) which shows that
> for 435 structures the corr coeff between resolution
> and average b is only 0.06, i.e. insignificant
>
> the only non-trivial correlate (using a 0.2 cut-off)
> is the percentage of secondary structure (makes
> sort of sense) with cc=0.20
>
> in my other large-scale test, mentioned a couple
> of weeks ago, i found that essentially all temp-
> factor-related staistics are "incorrectly"
> correlated with measures of model accuracy
> (e.g., higher average b tends to be accompanied
> by higher accuracy !). average b is very strongly
> correlated with completeness on the other hand.
> i suspect that problems with data and/or restraints
> (rather than physics) are a major determinant
> of the temp-factors we calculate for our models ...
>
> --dvd
>
>
> On Thu, 4 Jan 2001, Yu Wai Chen wrote:
>
> > *** For details on how to be removed from this list visit the ***
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> >
> > Dear all,
> >
> > Does any one know if there is any correlation between the overall
> > B-factor of a structure in relation to its resolution? Are there any
> > publications on this topic?
> >
> > Also is there any correlation between the extent of disorder in a
> > structure and the R-factor/Rfree?
> >
> > Thanks.
> >
> > Wai
> > --
> > ===================================================================
> > Yu Wai CHEN, Ph.D. .................. email:ywc@mrc-lmb.cam.ac.uk
> > Centre for Protein Engineering, tel:+44-(0)1223-402148
> > MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140
> > WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc
> >
>
> ******************************************************************
> Gerard J. Kleywegt
> Dept. of Cell & Molecular Biology Bolshevik University of Uppsala
> Biomedical Centre Box 596
> SE-751 24 Uppsala SWEDEN
>
> http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
>