[phenixbb] An easier explanation of the regions in omit map

Nathaniel Echols nechols at lbl.gov
Mon May 17 12:04:03 PDT 2010

On Mon, May 17, 2010 at 10:53 AM, xaravich ivan <xaravich.ivan at gmail.com>wrote:

> So I have quite a few regions build by the SA_omit map of phenix. But How
> do I go about looking at these maps. What am I looking for here. Should I
> look at the regions where the occupancy was set zero in all these outputs
> and find if I could build some thing from one of the maps? I guess I am
> asking, How do I use this information to move forward in refinement? There
> are 24 regions map and .pdb output in the /OMIT directory.

Ignore these - only the final map is useful.  If you are generating a
composite omit map, you want to make sure that what you've built still
matches the density reasonably well.  Obvious things to look at:

- flexible or missing loops
- ligands
- anywhere the mFo-DFc map shows large blobs at +/- 3sigma
- any outliers flagged by validation (both geometry and real-space

I don't usually find it productive to go through the structure
residue-by-residue, but this may depend on the data and model quality.  What
is your resolution and current R-free?

(If you are just omitting part of the structure, then you only need to look
at the map around those atoms - the rest won't be much different.)

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