[phenixbb] omit map

Ed Pozharski epozh001 at umaryland.edu
Fri Jun 3 09:47:27 PDT 2011

On Fri, 2011-06-03 at 11:41 -0400, Desi Mail wrote:
> But the 2Fo map around the ligand without omit is well defined.
> Phenix defines a very big box around the target pdb-includes
> surrounding protein residues. Is there a way to control this?
> The omit map of the water molecule in the binding site is also poor.

BTW, do you mean 2Fo-Fc map, not 2Fo?  And what exactly you mean by poor

Don't know if the box size can be changed, but if you want to omit just
the ligand, follow Jacob's suggestion - omit the ligand and run
simulated annealing to remove bias.

In theory, the observed behavior suggests model bias.  What's the

"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs

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