[phenixbb] B factor refinement in recent versions of phenix

Gino Cingolani Gino.Cingolani at jefferson.edu
Thu Aug 30 09:47:42 PDT 2012

Yes, I've had the same problem, too with two different structures. My solution to fix this is quite crude... before defining TLS groups, I remove 'zero' b-factors by hand  (e.g. vi myfile.pdb searching /1.00  0.0 which gives all B-factors set to zero). This started when I upgraded to the latest phenix (1.8-1069), and going back in time, 
it doesn't seem to happen with 1.7 versions.
Thanks for looking into this,


Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
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("You were not born to live like brutes, but to follow virtue and knowledge") Dante,
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From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Phil Jeffrey [pjeffrey at princeton.edu]
Sent: Thursday, August 30, 2012 12:39 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] B factor refinement in recent versions of phenix

I was battling this same problem this morning, whereby the <B> of the
structure is low and generating B-factors that are close to zero in many
instances.  This is at 2.6A where I don't generally expect issues with
systematically low B-factors.

Phil Jeffrey

On 8/30/12 11:52 AM, Pavel Afonine wrote:
> Hi Oliver,
> p.s.: I see you actually tried one of the latest versions (I missed it
> in my previous reply). Can you try this:
> 1) reset all B-factors to average or simply used the model where
> B-factors are "nomral" (not "too" small); then
> 2) run phenix.refine with this model.
> If this does not help then please send me the inputs so I can reproduce
> this and see what's happening.
> Thanks,
> Pavel
> On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
>> Hello,
>> I am experiencing a weird problem with B factor refinement
>> (individual, isotropic) in phenix.refine.
>> The dataset reveals a Wilson B factor of about 23 A². However, if
>> phenix.refine is allowed to run for a number of macrocycles, the mean
>> B value of the model drops continuously to about 9 A². In the end,
>> several atoms are getting values of 0.00!
>> There are no obvious abnormalities in the electron density, and R
>> values are quite good.
>> I was able to dig out an old phenix version (1.7.1) and found that
>> this one behaves perfectly well: mean B around 26 A² (slightly above
>> Wilson B, as is observed frequently) and minimum B around 10 A².
>> So obviously something has happened between versions 1.7.1 and 1.8 ...
>> The latest dev release (1143) shows the same behavior as version 1.8.
>> I should say that this structure is somewhat peculiar
>> (pseudomerohedral twinning plus twofold NCS), but again, the old
>> phenix version handles that without problems.
>> Moreover, the tendency for unreasonably low B factors has been
>> observed recently for a more "conventional" structure in our lab.
>> Any ideas what might be causing this and how to revert to the original
>> behavior?
>> Thanks in advance
>> Oliver
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