[phenixbb] difference map

Pavel Afonine 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.


More information about the phenixbb mailing list