Re: [ccp4bb]: Alternate side chains..

[<rams@poori.biochem.uiowa.edu>]

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


An interesting method is hidden in this paper


Kavanaugh JS, Weydert JA, Rogers PH, Arnone A.
Biochemistry 1998 Mar 31;37(13):4358-73


To the best of my knowledge this is the best way of calculating reliably 
the effect of a local change..


Rams.


On Wed, 4 Dec 2002, Gerard DVD Kleywegt wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> > Have people seen an improvement in R-factor and R-free following addition of 
> > alternate sidechains to their structures ?
> > Could you pl. share your experience since I dont see any change and I wonder 
> > what's going on.
> 
> R and Rfree are not the most suitable statistics to judge the
> addition of a handful of scatterers since they are global
> statistics. see, e.g., the following papers:
> - http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=32
> - http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=37
> - http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=56
> 
> --dvd
> 
> ******************************************************************
>                         Gerard J.  Kleywegt
>     [Research Fellow of the Royal  Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology  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.
> ******************************************************************
> 
> 

-- 
S. Ramaswamy
Department of Biochemistry.
University of Iowa.