Hi,
Hi i am trying to calculate a difference map ( ligand-native ) using isomorphous difference map program in phenix. I used the reflection files of ligand and native and phase information of ligand derived data. But the difference map donot fits the ligand, and appears as a circular chunk of density at sigma level 5.
I afraid this is one of the situations where I need to have the data to say something useful. If you send me the data (off-list of course) I will tell what is going on.
I calculated an omit map that clearly showed the presence of my ligand at the specific position.
If (unbiased) OMIT map shows the ligand why one would need to do anything else? You are done, I would say.
Is there anything wrong in my calculation. What alternate ways are there to improve my difference map.
Improving the difference density map is not the goal of structure solution. I can list a fair number of things you can try to do, but why? If the residual map shows the ligand then build it into it. Pavel.