Re: [ccp4bb] B-factor standardization
> 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. This will make some of BS negative (if B
Re: [ccp4bb] B-factor standardization
Dear Oliviero, On one aspect of your query, this analysis dissected the different sources of disorder contributions to B factors:- Diamond, R Acta Cryst (1990). *A46*, 425-435 All best wishes, John On Thu, Apr 5, 2018 at 2:49 PM, Oliviero Carugo < oliviero.car...@univie.ac.at> 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. > > Does anyone can help me in finding a publication (80s or 90s) where these > BS values are used? > > Thanks! > > Oliviero > -- Professor John R Helliwell DSc
Re: [ccp4bb] B-factor standardization
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
Re: [ccp4bb] B-factor standardization
Oliviero, We published a paper in 2003 in which we normalized B-factors to do a comparison of relative mobility or flexibility. The reference is: Gourinath et al. Structure 11:1621-1627 (2003). The jargon we used for Bave of the protein is . In our case, to be conservative in our interpretation of B-factor comparisons, we excluded random turns from the calculation and only included alpha helices and beta sheets, because we were trying to get a handle on the degree of excess flexibility of the less ordered regions of a large structure. -Daniel On Thu, Apr 5, 2018 at 9:49 AM, Oliviero Carugo < oliviero.car...@univie.ac.at> 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. > > Does anyone can help me in finding a publication (80s or 90s) where these > BS values are used? > > Thanks! > > Oliviero >
[ccp4bb] B-factor standardization
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. Does anyone can help me in finding a publication (80s or 90s) where these BS values are used? Thanks! Oliviero
