[phenixbb] Unusually low B factors

Nathaniel Echols nechols at lbl.gov
Wed Apr 17 12:49:43 PDT 2013

On Wed, Apr 17, 2013 at 12:41 PM, Brennan Bonnet
<Brennan.Bonnet at lightsource.ca> wrote:
> I could try this again if I need the newer version.  I'm currently completing my thesis and have processed and reprocessed this data so many times that.  At this point it's getting more important that I wrap up my degree than getting this processing to work 100%.
> I'm hoping that someone else has had this problem with B values before and could offer an explanation like "It's due to gas pressure, or sometimes B values are just low and that's acceptable".  That way I can include it in my thesis so that I don't get grilled by my committee.

Well, there is natural variability in the B-factors at any resolution,
and no direct equivalence to the Wilson B-factor calculated from
intensity statistics.  But the behavior you are seeing is an
implementation detail of some versions of Phenix - it all depends on
whether the overall scale is incorporated into the atomic B-factors.
Because most refinement programs (including most versions of Phenix
aside from a few of the 1.8 series) always do this, most
crystallographers have come to expect a specific range for B-factors
at any given resolution.  If you want to be absolutely certain that
your committee is happy, just re-run the last round of refinements
with the nightly build version - no need to do any re-processing or
anything fancy.


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