[phenixbb] B factor

[Pavel Afonine]

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.