[phenixbb] B factor

Pavel Afonine pafonine at lbl.gov
Sun May 11 10:45:21 PDT 2008

Hi Jianghai,

I see now. The problem is that if you do individual B-factors refinement 
(no TLS) then the result will be affected by restraints. Ideally you 
would need to do this without restraints, but this is not practical.

To obtain the estimate you want I would simply do group B-factors 
refinement with one B per residue. In this case the restrains are not 
used. It would be good to compare the results with TLS and individual 
only refinement. Do it in two steps: re-set all B to Wilson B (or to 
current average), then do group B refinement:

1) phenix.pdbtools model.pdb set_b_iso=25
2) phenix.refine model_b25.pdb data.mtz strategy=group_adp
Note, the default is one B per residue. You can specify your own selections.


On 5/11/2008 7:00 AM, Jianghai Zhu wrote:
> Pavel,
> Thanks.  I actually just want to do a very simple thing.  In the days  
> before TLS refinement, we use B-factor distributions to find the  
> ordered and less ordered regions in the structure, i.e.  low B- 
> factors, ordered region and high B-factors, less ordered region.  I  
> just wondered if I can still do that with the isotropic equivalent B- 
> factors after a TLS refinement.  Or should I just get a real isotropic  
> B-factors distribution by re-refining the model without TLS?
> -- Jianghai
> On May 11, 2008, at 2:03 AM, Pavel Afonine wrote:
>> Hi Jianghai,
>>> If I compare the isotropic equivalent B-factor
>>> after TLS refinement to the isotropic B-factor without TLS  
>>> refinement,
>>> will they have the same trend?
>> yes, only if:
>> 1) the choice of TLS groups is correct;
>> 2) the restraints on isotropic individual B-factors are not too tight.
>>> I want to use the B-factor
>>> distribution to describe the ordered and disordered region in the
>>> structure, will the TLS refinement skew that?
>> I'm not sure what exactly you want to do here. But anyway, by using  
>> TLS
>> model you better describe atomic ADP: TLS models global domain motion
>> and individual B-factors model local atomic vibrations; that is each
>> kind of motion receives dedicated parameterization (which is good).
>> However, if you model everything with individual B-factors (no TLS)  
>> the
>> similarity restraints are always used and they tend to remove TLS
>> contribution making final B-factors less adequate.
>> Pavel.
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