[phenixbb] omit map

[Ed Pozharski]

You may want to adjust contouring level

On Fri, 2011-06-03 at 13:23 -0400, Mary wrote:
> 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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-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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