[phenixbb] zero B-factors
pafonine at lbl.gov
Mon Nov 18 12:03:51 PST 2013
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.
> * * * * * * * * * * * * * * * * * * * * * * * * * * * *
> 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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