[phenixbb] B factor refinement in recent versions of phenix

"Weiergräber, Oliver H." o.h.weiergraeber at fz-juelich.de
Thu Aug 30 08:35:17 PDT 2012


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

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

More information about the phenixbb mailing list