[phenixbb] zero B-factors

Engin Özkan 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.

Engin

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.
>
> 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.
>>
>>
>>
>>     _________________________________________________
>>     phenixbb mailing list
>>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>>     http://phenix-online.org/__mailman/listinfo/phenixbb
>>     <http://phenix-online.org/mailman/listinfo/phenixbb>
>>
>>
>>
>>
>> -- 
>> Morten K Grøftehauge, PhD
>> Pohl Group
>> Durham University
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb



More information about the phenixbb mailing list