[phenixbb] B-iso vs. B-aniso

Pavel Afonine pafonine at lbl.gov
Tue Sep 18 14:00:58 PDT 2012

Hi Yuri,

> The protein model I am refining has 400 amino acids (3320 atoms).
> Some real quick calculations tell me that to properly refine it 
> anisotropically, I would need 119,520 observations. Given my unit-cell 
> dimension and space-group it is equivalent to about a 1.24 A complete 
> data set.

interesting how you managed to do this... In any case this number is 
likely to be useless as refinement target uses both, X-ray term and 
restraints accounted with some weight.

There are various rules of thumb that are typically specific to 
refinement programs you use.. Depending on data and model quality you 
can refine all non-solvent atoms with anisotropic ADPs starting from 
about 1.7-1.5A and higher. At about 1.2A and higher you can refine 
solvent with anisotropic ADPs as well. Again, data quality and where you 
currently are with refinement is important.

> However, I have had a couple of cases where anisotropic B-factor 
> refinement significantly improved R-work and R-free, while maintaining 
> a reasonable R-gap, for lower resolution models (1.4-1.5 A, around 
> 70,000 reflections). What is the proper way of modelling the B-factors?

Try the above rules of thumb and see what pleases the R-factors (both, 
work, free and gap) and makes sensible ADPs. In gray areas, like "1.7A 
resolution great data" or "1.4A heavily incomplete data" try multiple 
plausible options. That's the most robust way to find the answer.


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