[phenixbb] difference map

det102 at uoxray.uoregon.edu det102 at uoxray.uoregon.edu
Wed Feb 9 21:50:29 PST 2011

    This is a long shot, but it's possible that you calculated a
Fapo-Fligand map instead of the other way 'round.  Normally you
would have a positive peak surrounded by a negative ripple (due
to series termination and other factors).  If you get the F's
reversed the negative ripple becomes positive and the ligand
density becomes negative.  What does you negative contour say?

Dale Tronrud

On 2/9/2011 7:33 PM, intekhab alam wrote:
> 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 calculated an omit map that clearly showed the presence of my ligand at the specific position. Is there anything wrong in my calculation. What alternate ways are there to improve my difference map.
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