Difference Map positive peaks in release dev-798
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. -- Yuri Pompeu
Hi Yuri, can you send me the complete set of files so I can reproduce the problem myself: - 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. Thanks, Pavel. 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.
participants (2)
-
Pavel Afonine -
Yuri