[phenixbb] difference map

Pavel Afonine pafonine at lbl.gov
Wed Feb 9 22:40:02 PST 2011


the current version of Fo-Fo map calculation in PHENIX 
(phenix.fobs_minus_fobs_map) requires the unit cell parameters to be 
nearly identical, otherwise it would not run. So if it runs (according 
to Intekhab) then we can safely assume that this is the case.

It's a good idea to make sure to contour the map at correct levels (or 
make sure the order in Fo1-Fo2 is right) as Dale suggested. Otherwise it 
is strange that the Fo-Fo map doesn't show anything, while residual map 
does show the ligand...

Anyway, if unbiased Fo-Fc map shows the ligand then I don't see why one 
would struggle with something else instead of just using this map to 
build the ligand.


On 2/9/11 8:04 PM, Thomas C. Terwilliger wrote:
> 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
> model.
> 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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