Re: [ccp4bb]: B-factor and resolution

["Gerard \"CD\" Kleywegt" <gerard@xray.bmc.uu.se>]

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


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  ***
> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> 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.
******************************************************************