[phenixbb] Fo-Fc omit map for ligand in the protein-ligand structure

Pavel Afonine pafonine at lbl.gov
Tue Sep 16 09:22:11 PDT 2014

Hi Dale,

your points are all very good!

Let's have a look at this at a different angle though. Bulk-solvent is 
part of the model: it is the model for the other "half" of the unit cell 
volume that is not interpreted in terms of individual atoms.

If ligand is not built yet this means the program will use an incorrect 
model (bulk-solvent) to describe ligand's region. Isn't it introducing a 
bias?! I would think so.


On 9/15/14 11:41 AM, Nathaniel Echols wrote:
> On Mon, Sep 15, 2014 at 8:58 AM, Dale Tronrud <detBB at daletronrud.com 
> <mailto:detBB at daletronrud.com>> wrote:
>        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.
> Agreed - this is much easier than placing the ligand and then having 
> to run SA.  I suspect this is a case where "oral tradition" has been 
> misinterpreted, since everyone is told that the SA omit map is the 
> "standard" for showing unbiased difference density, and they don't 
> realize that it's better to simply avoid the bias to begin with.
> -Nat
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