[phenixbb] zero B-factors

Morten Grøftehauge mortengroftehauge.work at gmail.com
Mon Nov 25 04:29:51 PST 2013

It would be nice if the validation procedures looked for B-factor outliers
that were too low as well as too high. A very low B-factor can be
indicative of the wrong atom, e.g. a water molecule that is actually an ion.


On 18 November 2013 21:38, Pavel Afonine <pafonine at lbl.gov> wrote:

> If you see this problem using the latest Phenix version then please send
> me files (off-list) necessary to reproduce it and I will investigate.
> If interested what was the "problem" causing zero B-factors please see
> below.
> Thanks,
> Pavel
> In a nutshell the problem is this. Assuming total model structure factor
> is (for simplicity):
> F ~ exp(-Boverall_scale * s**2) * exp(-Batoms * s**2)
> it's clear that any combination of Boverall_scale and Batoms that
> maintains Boverall_scale+Batoms=const will not change total model structure
> factors (and therefore R-factors, maps, etc).
> The new bulk-solvent and overall scaling algorithm that we implemented
> sometime in April 2012 and that went into 1.8_1069 originally did not care
> about returning isotropic component of Boverall_scale back to atoms
> (Batoms):
> http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf
> In fact, it assumed that overall contribution (overall B that is equal for
> all atoms) should stay in Boverall_scale (indeed, why keep common B in all
> individual atomic B-factors!?), and the rest goes into Batoms.
> This behavior typically generates user concerns about "too small"
> B-factors.
> An alternative agreement is to postulate that the matrix Boverall_scale is
> traceless meaning that overall B-factor goes into individual atomic
> B-factors.
> This behavior occasionally generates user concerns about "too large"
> B-factors.
> A few months later (sometime in end summer/fall 2012) we changed scaling
> behavior such that overall B-factor stays in individual atomic B-factors.
> All in all, either way is correct and a matter of agreement and
> preferences, but definitely not a bug.
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Morten K Grøftehauge, PhD
Pohl Group
Durham University
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