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 ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: [email protected] Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ________________________________________ From: [email protected] [[email protected]] on behalf of Phil Jeffrey [[email protected]] 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 Princeton 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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