[phenixbb] zero B-factors
Edna Patricia Matta, Ms
edna.matta at mail.mcgill.ca
Mon Nov 18 12:33:01 PST 2013
Thanks a lot for all the answers :)
Pavel was very kind to re-run my data with the latest version of the software and the problem was solved!!
A great week to all,
Edna Patricia Matta, MSc. PhD
Goodman Cancer Centre
1160 Pine Avenue West, Room 614
Montreal, Quebec, CANADA, H3A 1A3
[http://www.med.mcgill.ca/nahum/images/tel.png] TEL: 1-514-398-7275
[http://www.med.mcgill.ca/nahum/images/fax.png] FAX: 1-514-398-1287
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Anshul Bhardwaj [Anshul.Bhardwaj at jefferson.edu]
Sent: Monday, November 18, 2013 3:02 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] zero B-factors
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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