[phenixbb] difference map

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Feb 9 20:04:06 PST 2011

Hi Intekhab,

I would first examine the cell of your native and ligand-bound structures.
If these are very similar (much less than 1% different) then I would be
surprised by the results, and would try to make sure that everything is
working as expected.

If the cells are rather different (>2%) then the results are plausible
(though I don't exactly understand the "circular chunk of density"). In
this case, I would use the 2mFo-DFc map from your refined ligand-bound
structure as your map.  It would be good to refine without the ligand (or
even better to not put the ligand in at all until you have good density
for it.)

If the cells are only somewhat different (1%) then either of the two above
possibilities might hold.

Normally an omit map doesn't help to show a ligand if you did not put the
ligand there in the first place.  Omit maps are good for finding what is
wrong with a model, not so good for finding things that are not in your

All the best,
Tom T

>> 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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