Yes. It is 2Fo-Fc map. The resolution is 1.36 with 97% completeness.<br>I have attached three small screen shots to clarify your suggestions.<br>lig density-ref11.tif- 2Fo-Fc map before ligand fitting<br>lig omit density.tif - map after omitting the ligand from the final pdb.<br>
density-no lig.tif - map without the ligand using the final pdb<br><br>Thanks<br>Mary<br><br><br><div class="gmail_quote">On Fri, Jun 3, 2011 at 12:47 PM, Ed Pozharski <span dir="ltr"><<a href="mailto:epozh001@umaryland.edu">epozh001@umaryland.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">On Fri, 2011-06-03 at 11:41 -0400, Desi Mail wrote:<br>
> But the 2Fo map around the ligand without omit is well defined.<br>
> Phenix defines a very big box around the target pdb-includes<br>
> surrounding protein residues. Is there a way to control this?<br>
><br>
> The omit map of the water molecule in the binding site is also poor.<br>
><br>
<br>
</div>BTW, do you mean 2Fo-Fc map, not 2Fo? And what exactly you mean by poor<br>
density?<br>
<br>
Don't know if the box size can be changed, but if you want to omit just<br>
the ligand, follow Jacob's suggestion - omit the ligand and run<br>
simulated annealing to remove bias.<br>
<br>
In theory, the observed behavior suggests model bias. What's the<br>
resolution?<br>
<font color="#888888"><br>
--<br>
"I'd jump in myself, if I weren't so good at whistling."<br>
</font><div><div></div><div class="h5"> Julian, King of Lemurs<br>
<br>
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