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<p>Hello Edna,</p>
<p>I am in the same boat, I had similar <b>B-factor=0 problem with phenix.refine ver. 1.8_1069</b>. 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
<b>PHENIX version 1.8.4-1496</b>, that<b> </b>takes care for the problem.</p>
<p>Hope this helps!<br>
</p>
<p>Best,</p>
<p>Anshul</p>
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<div style="font-family:Tahoma; font-size:13px"><font color="black" face="Tahoma" size="2"><span dir="ltr" style="font-size:10pt"><font face="Arial" size="2">Anshul Bhardwaj, Ph.D.<br>
Faculty, Department of Biochemistry and Molecular Biology <br>
Manager, Kimmel Cancer Center X-ray Crystallography and Molecular Interactions<br>
Thomas Jefferson University<br>
233 South 10th Street, BLSB suite 822 <br>
Philadelphia, PA 19107<br>
Tel: (215) 503-4587<br>
anshul.bhardwaj@jefferson.edu<br>
http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html
<br>
http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm</font><br>
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<div id="divRplyFwdMsg" dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b> phenixbb-bounces@phenix-online.org <phenixbb-bounces@phenix-online.org> on behalf of Edna Patricia Matta, Ms <edna.matta@mail.mcgill.ca><br>
<b>Sent:</b> Saturday, November 16, 2013 12:37 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] zero B-factors</font>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt"><font size="2"><font face="Helvetica" size="3">Hello,<br>
<br>
Recently I did submit a structure to the PDB but they found that some atoms had zero value for the B-factors.<span style="font-size:10pt"><br>
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.
</span>I used Phenix 1.8.<br>
<br>
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.<br>
<br>
Somebody can help me?<br>
Thanks a lot,<br>
Edna</font><br>
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