[phenixbb] zero B-factors

Diana Tomchick Diana.Tomchick at utsouthwestern.edu
Mon Nov 18 11:45:00 PST 2013

I have had this problem in the past for refinement of some low resolution datasets. The problem resolved itself when I elected to optimize both the X-ray/stereochemistry and the X-ray/ADP weights. It adds some time to the refinement cycles, but I always have lots of other things to do while I'm waiting for the job to finish.

If you are using the Phenix GUI, then look under the refinement results "Atomic properties" tab which reports ADP statistics. This should provide you a listing of atoms with problematic ADP values.


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Diana R. Tomchick
University of Texas Southwestern Medical Center
Department of Biophysics
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816, U.S.A.
Email: Diana.Tomchick at UTSouthwestern.edu
214-645-6383 (phone)
214-645-6353 (fax)

On Nov 15, 2013, at 11:37 PM, Edna Patricia Matta, Ms wrote:

> Hello,
> 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
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> phenixbb at phenix-online.org
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