On Thursday, 05 April 2018 15:49:44 Oliviero Carugo wrote:
> Dears,
>
> everybody knows that B-factors may change amongst different crystal
> structures and that they need to be standardized when different protein
> crystal structures are compared.
>
> If I am not wrong, I remember that someone proposed to standardize
> B-factors of protein atoms as “BS = B - Bave”, where Bave is the average
> B-factor of the protein. Such standardization is based on the hypothesis
> that independent sources of disorder add in determining the final
> B-factor. BS should represent atomic B-factors depurated by all factors
> different from atom oscillation, since Bave differences are neutralized.
That sounds like flawed logic to me.
If you were going to do this at all, I think you would have to
start by comparing the residual B factors after removing TLS
contributions.
> Does anyone can help me in finding a publication (80s or 90s) where
> these BS values are used?
I think there are better tools available now than there were
25 years ago. I wouldn't go back that far to choose one without
first considering the work and thought that has been put into
structure analysis in the meantime. If nothing else, you might
consider that "Bave" as calculated from the "Biso" (really Beq)
column in typical PDB files is a less than perfect approximation
[Acta Cryst. 2012 A67:512-516]
Ethan
> Thanks!
>
> Oliviero
--
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
