[phenixbb] zero B-factors
Diana.Tomchick at utsouthwestern.edu
Mon Nov 18 13:01:35 PST 2013
Then this bug has been around for quite some time, as the last version that caused it for me was 220.127.116.119 (which was released in February of this year).
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Diana R. Tomchick
University of Texas Southwestern Medical Center
Department of Biophysics
5323 Harry Hines Blvd.
Dallas, TX 75390-8816, U.S.A.
Email: Diana.Tomchick at UTSouthwestern.edu
On Nov 18, 2013, at 2:03 PM, Pavel Afonine wrote:
> all it needs to resolve this particular problem is not use an ancient Phenix version (that has that feature).
> Edna's problem was solved after switching from 1.8_1069 (which I consider ancient) to a more recent (in fact latest) version.
> On 11/18/13 11:45 AM, Diana Tomchick wrote:
>> 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:
>>> 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,
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>> UT Southwestern Medical Center
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