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.

Pavel

On 9/15/14 11:41 AM, Nathaniel Echols wrote:

On Mon, Sep 15, 2014 at 8:58 AM, Dale Tronrud <[email protected]> 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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