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
Postdoctoral Fellow
McGill University
Goodman Cancer Centre
1160 Pine Avenue West, Room 614
Montreal, Quebec, CANADA, H3A 1A3
TEL: 1-514-398-7275
FAX: 1-514-398-1287Sent: Monday, November 18, 2013 3:02 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] zero B-factors
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!
Best,
Anshul
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
[email protected]
http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html
http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm
Sent: Saturday, November 16, 2013 12:37 AM
To: [email protected]
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,
Edna
|
The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution
or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
|