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

Nathaniel Echols nechols at lbl.gov
Mon Sep 15 11:41:05 PDT 2014

On Mon, Sep 15, 2014 at 8:58 AM, Dale Tronrud <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.

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