[phenixbb] zero B-factors

[Engin Özkan]

I was looking at this histogram when I wrote that email :) but that 
histogram is not clickable and does not report residue names (unlike the 
list just below it). I always look at the histogram (and its usually 
Poisson-like shape is intriguing). It was just a suggestion to add the 
other end of the distribution to the list of outlier residues reported 
by Phenix.

Engin

On 11/25/13, 10:12 AM, Pavel Afonine wrote:
> Engin,
>
> you can see it as a histogram. Also phenix.refine log shows histograms 
> of B-factors that will capture this.
>
> Most of the time the problem is not about not having the information 
> but not knowing what to look for or not willing to look. Then 
> eventually overlooked problems get discovered later down the road by 
> someone else.
>
> Pavel
>
> On 11/25/13 7:59 AM, Engin Özkan wrote:
>> 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
>>>>
>>>>
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