Re: [ccp4bb]: B factors

[<wgscott@chemistry.ucsc.edu>]

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

I have a 3 Angstrom resolution structure that refined in CNS with a 
<B>=78 A**2 and an Rfree of almost 30% and using Refmac <B>=42 A**2 and 
Rfree of 23% (keeping the same test/working set division and starting 
model and similar geometric deviations from ideality).

I worry that something might be going wrong with the CNS bulk solvent 
model in CNS, or that there might be some other problems.


On Friday, December 13, 2002, at 12:02 PM, Michael Strickler wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Edward Berry wrote:
>
>> I would also be interested in the current opinion(s). Speaking for
>> myself, I think that 80 or 100 is a very reasonable average atomic B
>> for structures diffracting to low resolution, and the relative 
>> scarcity
>> of such high B-factors in the PDB is due to questionable practices 
>> used
>> in the past which did not preserve the overall B-factor information
>> present in the original data.
> .....
> .....
>
> When we first started using maximum-likelihood refinement *COUGH* in 
> CNS *COUGH*, we noticed that both R-factors and B-factors were coming 
> out higher than we were used to.  It took some hard selling to the 
> Powers That Be to convince them that this was probably a symptom of 
> "questionable practices" in previous refinement methods.  I've since 
> noticed (anecdotally) more frequent occurrences of B-factors that we 
> once would have called abnormally high based on our strange old rules 
> of thumb, such as that main-chain B's should be around 20.  This rise 
> in temperature factors often seems, IMHO, to correspond to a rise in 
> understanding, and avoidance, of model bias during refinement.  Then 
> again, my grip on reality is often tenuous.
>
> Just My Two Pence,
> -- 
> Michael Strickler, Ph.D.
> Research Specialist
> Center for Structural Biology
> Howard Hughes Medical Institute
> Yale University
>
>
>
William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)