Thanks for the friendly help for the sometimes clueless! It's working. <br><br><div class="gmail_quote">On Fri, Nov 4, 2011 at 12:49 PM, Nigel Moriarty <span dir="ltr"><<a href="mailto:nwmoriarty@lbl.gov">nwmoriarty@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Laurie<br>
<br>
You should add the metal and waters to your model, then you can run<br>
either ReadySet! or phenix.metal_coordination (which is used in<br>
ReadySet!) to get an "edits" file for passing to phenix.refine. The<br>
script looks for isolated metals (not Fe in Heme, eg) and determines<br>
the coordination sphere. The distance cutoff can be adjusted. The bond<br>
lengths are taken from a lookup table while the angles are taken from<br>
the input geometry. You should probably not include the angles when<br>
the structure is not well refined so you can edit the "edits" or use<br>
an option to phenix.metal_coordination.<br>
<br>
Nigel<br>
<div><div></div><div class="h5"><br>
On Fri, Nov 4, 2011 at 9:06 AM, Laurie Betts <<a href="mailto:laurie.betts0508@gmail.com">laurie.betts0508@gmail.com</a>> wrote:<br>
> How does PHENIX know where to look for proper bond lengths and angles for a<br>
> metal ion I add to a protein structure - do I just add the metal into<br>
> difference density and any waters, and then run ready set and it knows where<br>
> to look for that particular metal and the atoms to which is is coordinated?<br>
> And shouldn't there be a 'cif file that it outputs, or is that something<br>
> that I need to get myself? Sorry it's still not obvious to me from the<br>
> documentation.<br>
><br>
> Thanks<br>
><br>
> Laurie Betts<br>
><br>
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<br>
</div><font color="#888888">--<br>
Nigel W. Moriarty<br>
Building 64R0246B, Physical Biosciences Division<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : <a href="tel:510-486-5709" value="+15104865709">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>
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