[phenixbb] zero B-factors

Anshul Bhardwaj Anshul.Bhardwaj at jefferson.edu
Mon Nov 18 12:02:10 PST 2013

Hello Edna,

I am in the same boat, I had similar B-factor=0 problem with phenix.refine ver. 1.8_1069. Apparently, it was a bug in that specific version of PHENIX, which was fixed subsequently in later versions. Almost more than a year after PDB deposition to RCSB database, RCSB annotators found the issue and requested to send revised PDB with properly refined B-factors. The simplest solution is to refine the structure with latest official stable PHENIX version 1.8.4-1496, that takes care for the problem.

Hope this helps!



Anshul Bhardwaj, Ph.D.
Faculty, Department of Biochemistry and Molecular Biology
Manager, Kimmel Cancer Center X-ray Crystallography and Molecular Interactions
Thomas Jefferson University
233 South 10th Street, BLSB suite 822
Philadelphia, PA 19107
Tel: (215) 503-4587
anshul.bhardwaj at jefferson.edu

From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Edna Patricia Matta, Ms <edna.matta at mail.mcgill.ca>
Sent: Saturday, November 16, 2013 12:37 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] zero B-factors


Recently I did submit a structure to the PDB but they found that some atoms had zero value for the B-factors.
I am new in this filed and I do not know what to do. There have been reports of problems with some versions of phenix about this. I used Phenix 1.8.

I repeted the refinement doing restrain NCS-related B-factors but I do not find where to check for the the B-factor values in the the log file.

Somebody can help me?
Thanks a lot,

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