[phenixbb] whether phenix.refine can do Boverall refinement

Pavel Afonine pafonine at lbl.gov
Thu Mar 31 15:21:05 PDT 2011

Hi Hailiang,

> I ccp4-refmac, there is a "BREF OVER" mechanism to refine the overall
> B-factor (Boverall, obtained from scaling is added to the atomic B values,
> or,
> http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#refi_bref).
> I am just wondering in phenix.refine, whether we could do this after
> positional and tls refinement. It seems to me the Boverall corresponds to
> the overall anisotropic scaling factor and will be refined prior to any
> positional/B-factor refinement in phenix.refine by default. I may be
> wrong, but if not, my question was whether we could do it afterward.

this is described in great details here:


see article "On atomic displacement parameters ...". In this article 
it's called Ucryst. I guess this is more or less what is called Boverall 
in Refmac.


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