[phenixbb] B factor

Jianghai Zhu jzhu at idi.harvard.edu
Sun May 11 07:00:10 PDT 2008


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  
> 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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