[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

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