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
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Kennen Sie schon unsere app? http://www.fz-juelich.de/app _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb