[phenixbb] zero B-factors

[Pavel Afonine]

Hi Morten,

POLYGON is the tool for this. Definition "too low/high" is relative and 
depends on resolution.

Pavel

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.
>
> Morten
>
>
> 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
>     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
>     <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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