[phenixbb] difference map
pafonine at lbl.gov
Wed Feb 9 20:47:24 PST 2011
> 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.
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