On Fri, Jun 3, 2011 at 12:47 PM, Ed Pozharski
<epozh001@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."