[phenixbb] high average b-factor vs. Wilson B - EXPLANATION

Pavel Afonine pafonine at lbl.gov
Fri Aug 6 13:17:48 PDT 2010

  Hi Phil,

Just to make sure I got your point correctly... Are you suggesting to 
add Bcryst to the total ADP as well (so it is always included into 
isotropic B in ATOM record and anisotropic b in ANISOU record), 
similarly to what we already do with TLS contribution?

If we do that:

- all atoms will always have ANISOU (because Bcryst is anisotropic);
- do you know how to convert Bcryst obtained in reciprocal space to the 
one in real space (so it can be added to individual ADP) (never thought 
about it - am I asking something stupid....?)?


On 8/6/10 12:58 PM, Phil Jeffrey wrote:
> 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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