[phenixbb] B-iso vs. B-aniso

Nathaniel Echols nechols at lbl.gov
Mon Sep 17 13:50:48 PDT 2012

On Mon, Sep 17, 2012 at 11:12 AM, Yuri <yuri.pompeu at ufl.edu> wrote:
> 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?

I have also seen the anisotropic refinement work very well at this
resolution, but there are certainly exceptions.  Pavel has recommended
that you leave the waters isotropic until about 1.2A, however (there
are shortcuts for setting the selections for this and other common
scenarios in the GUI).  At any rate, if you really want to be certain,
don't think there's any substitute for running the refinement both
ways, isotropic and anisotropic, and seeing which works best.  There
are probably different opinions on how to judge whether anisotropic
refinement is justified, but R-free should drop by at least 0.5%, and
1% is probably a more rigorous cutoff.  One of the recent PDB-REDO
papers had a description of their decision-making process for this,
which I thought seemed sensible (they're using REFMAC, not Phenix, but
the principle is the same in either case).


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