[phenixbb] simulated annealing omit map

Pavel Afonine pafonine at lbl.gov
Thu Nov 13 08:38:42 PST 2014

Hello Bishal,

as discussed before, computing ligand-omit map is tricky.

Quoting my previous email:

There are two commonly used options for omitting the ligand in order to 
demonstrate its presence/absence in Fo-Fc OMIT map:

1) Physically remove the ligand from PDB file. Then do some refinement 
and calculate Fo-Fc map.

2) Keep ligand in the file, set its occupancy to zero. Then, again, do 
some refinement and calculate Fo-Fc map. In this case you may want to 
ask refinement program to not move the ligand or move it only a little.

Now, here is why these two options are poor and will not give you what 
you want.

In the first case the bulk-solvent mask will be set in the ligand region 
and therefore it will mask ligand density (bulk-solvent will be filled 
into the ligand region). Depending on the strength of ligand density it 
may be masked completely or deteriorated.

If you follow the second option you will always get positive density in 
ligand area. This density may correspond to bulk-solvent, ligand or 
mixture of both. That is there will be no simple way to differentiate 
whether this density arises from the ligand or bulk-solvent.

Dale Tronrud offered a great alternative option:

An alternative you might want to consider is what I call the
"discovery map".  At some point in the refinement process there was a
map that convinced YOU that this ligand was present.  You should be
the hardest person to be convinced so that map will be both an omit
map (because the model had been refined without the ligand prior to
this) and clear enough to satisfy the reader.

Now, recently I improved composite OMIT map calculation in


tool, see picture that illustrates how it works:


I think at present that's the best option to follow if for some reason 
you cannot follow Dale's suggestion.


On 11/13/14 6:58 AM, Singh, Bishal wrote:
> Hello everybody,
>   I am generating figures showing the electron density map around the 
> ligands. I deleted the ligands from final co-ordinate file and then 
> performed refinement  with identical parameters as before while 
> keeping simulated annealing=true. I shall be thankful if someone could 
> suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. 
> Kindly also tell me the minimum acceptable contour level required for 
> showing difference map. All structures are at 1.4 - 2.0 angstrom 
> resolutions.
> Regards,
> Bishal 

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