[phenixbb] zero B-factors
eozkan at stanford.edu
Mon Nov 25 07:59:26 PST 2013
I think what was meant is Phenix report not only *residues* with
"suspiciously high B-factors" as it does in the GUI (thanks!), but also
those with suspiciously low. As said, one could then detect that one
water that was actually a big ion. The overall comparisons reported by
POLYGON are useful for determining refinement parameterization and such,
but not details like this.
On 11/25/13, 9:40 AM, Pavel Afonine wrote:
> Hi Morten,
> 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.
>> phenixbb mailing list
>> 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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