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

Phil Jeffrey pjeffrey at princeton.edu
Fri Aug 6 13:51:46 PDT 2010

Hi Pavel,

No, I was just suggesting that the trace of B-cryst be applied, in the 
same way that CNS does, so that less things are hidden in the header and 
that the B-iso for each atom would be the same as the effective B-iso 
for the atom after applying B-cryst.  In fact I'd assumed that was what 
phenix.refine did although obviously I had not thought to check.

If you added the anisotropic component of B-cryst I think it would cause 
more confusion than it resolves, since it will generate all those 
per-atom ANISOU entries even if no TLS or atomic anisotropic refinement 
was done, and nearly double the size of a PDB file.  My viewpoint is 
rather biased to what I historically "expect" to find in PDB file atom 
entries, however.


Pavel Afonine wrote:
>  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....?)?
> Thanks!
> Pavel.
> 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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