[phenixbb] zero B-factors
pafonine at lbl.gov
Mon Nov 25 07:40:01 PST 2013
POLYGON is the tool for this. Definition "too low/high" is relative and
depends on resolution.
On 11/25/13 4:29 AM, Morten Grøftehauge wrote:
> 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
> <mailto: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
> If interested what was the "problem" causing zero B-factors please
> see below.
> 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):
> 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"
> 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"
> 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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> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> Morten K Grøftehauge, PhD
> Pohl Group
> Durham University
> phenixbb mailing list
> phenixbb at phenix-online.org
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