[phenixbb] omit map

Mary desimail007 at gmail.com
Fri Jun 3 10:23:43 PDT 2011


Yes. It is 2Fo-Fc map. The resolution is 1.36 with 97% completeness.
I have attached three small screen shots to clarify your suggestions.
lig density-ref11.tif- 2Fo-Fc map before ligand fitting
lig omit density.tif - map after omitting the ligand from the final pdb.
density-no lig.tif - map  without the ligand using the final pdb

Thanks
Mary


On Fri, Jun 3, 2011 at 12:47 PM, Ed Pozharski <epozh001 at umaryland.edu>wrote:

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