[phenixbb] B factor refinement in recent versions of phenix - SUMMARY
pafonine at lbl.gov
Thu Aug 30 20:10:36 PDT 2012
this is just a summary..
In a nutshell the problem was following. Assuming total model structure
factor is (for simplicity):
Fmodel ~ exp(-Boverall_scale) * exp(-Batoms)
it's clear that Boverall_scale and Batoms are correlated, and any
combination of Boverall_scale and Batoms that maintains
Boverall_scale+Batoms=const will not change the the total model
structure factors (and therefore R-factors, etc).
The new bulk-solvent and overall scaling algorithm that I switched to in
April did not care about returning isotropic component of Boverall_scale
back to atoms:
In fact (as explained above), the new algorithm does not use analytical
form for overall scale at all.
Therefore a portion of Batoms was systematically absorbed by
Boverall_scale. Not sure if this is a real problem, but to be consistemt
with previous versions and expectations, recently (may be a month ago or
so) I changed it such that isotropic exponential component of overall
scale is added back to atoms. So current version of phenix.refine should
not produce these "too small" B-factors anymore.
Anyone who experience this problem please try the latest Phenix from
If this does not solve the problem please let me know. The most
efficient way to let me know is to send me data and model files so I can
reproduce and fix the problem.
On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
> I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine.
> The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00!
> There are no obvious abnormalities in the electron density, and R values are quite good.
> I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A².
> So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8.
> I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems.
> Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab.
> Any ideas what might be causing this and how to revert to the original behavior?
> Thanks in advance
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