Re: [ccp4bb]: B factors

[Michael Strickler <michael@mail.csb.yale.edu>]

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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