[phenixbb] Difference Map positive peaks in release dev-798
pafonine at lbl.gov
Sat Jun 25 22:24:59 PDT 2011
can you send me the complete set of files so I can reproduce the problem
- input data and model files, and parameter file (if any);
- the exact command that you used to run phenix.refine that results in
positive density on Mg in dev-798 and no density in 743?
Please send the files to my email (NOT the whole list). I will have a
look once I have the files.
On 6/25/11 10:04 PM, Yuri wrote:
> I just ran the same job using the last official release (743).
> Some differences:
>> When the change occurred (between which version numbers)?
> Some where in between 743 and dev-798.
>> Does the peak disappear if you do the same calculation using an older
> Yes, I see no positive or negative peaks for the Mg ion (nor my ligand).
>> There is no general remedy - it's all case-dependent.
>> Does its B-factor differ significantly from surrounding atoms?
> Yes, the B-factor for the ligand is 20 on average. The surrounding
> residues and cofactor are 10 or below.
> But, as I mentioned above, I see no positive peak density this time
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