[phenixbb] high average b-factor vs. Wilson B - EXPLANATION
Phil Jeffrey
pjeffrey at princeton.edu
Fri Aug 6 12:58:56 PDT 2010
Pavel Afonine wrote:
>
> in summary, in that email I wrote that there are two ways of how you can
> handle the total B-factor and one of its components (Bcryst). You can
> subtract the trace of Bcryst and add it to individual ADPs (what CNS
> does, for example) or you can keep Bcryst as it is. Both ways do not
> change the Fmodel and therefore the R-factors. So I can't see how you
> conclude from this about refinement stability. These are purely
> formatting/convention things.
Strikes me that the convention should be that the B-factors associated
with the atoms should be in the PDB B-factor field associated with those
atoms, subject to the ability to represent the ADP model. Burying a
constant isotropic offset in the PDB header - which might be of variable
format depending on what program is used - seems like a good way to get
the overall ADP of the model to be incorrectly assessed.
This would seem to be analogous to the difference between reporting the
equivalent total B-iso in the isotropic B-factor field in TLS refinement
(as phenix.refine does) versus reporting just the residual B (REFMAC
default behavior). i.e. all the information is in the PDB file
somewhere, but it's not necessarily where you expect it to be. I rather
prefer the phenix.refine method for this.
Since most of the interest with Wilson B seems to be comparing Fmodel
with the Fobs, it may make more sense to compare the Wilson B calculated
from Fmodel with the Wilson B calculated with Fobs, which might at least
cancel out some of the errors in the calculation. The underlying
question seems to be "does the distribution of |Fmodel| with resolution
match that of |Fobs|".
Phil Jeffrey
Princeton
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