[phenixbb] Difference Map positive peaks in release dev-798

Pavel Afonine pafonine at lbl.gov
Sat Jun 25 22:24:59 PDT 2011

Hi Yuri,

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:
> Pavel,
> 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 
>> version?
> 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 
> around.

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