[phenixbb] omit map

Nathaniel Echols nechols at lbl.gov
Fri Jun 3 08:47:18 PDT 2011

On Fri, Jun 3, 2011 at 8:41 AM, Desi Mail <desimail007 at gmail.com> wrote:

> But the 2Fo map around the ligand without omit is well defined.

Phase bias can do that sometimes... it might really be there, but you can't
trust the final refined maps too much.  What did the map look like before
you placed the ligand?

> Phenix defines a very big box around the target pdb-includes surrounding
> protein residues. Is there a way to control this?

Yes, instead of using AutoBuild for this, run phenix.refine with the default
strategy (tailored appropriately for your structure if necessary) plus
simulated annealing, using a model with the only ligand and any important
waters deleted.  The output map should be exactly what you want.

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