Laurie
You should add the metal and waters to your model, then you can run
either ReadySet! or phenix.metal_coordination (which is used in
ReadySet!) to get an "edits" file for passing to phenix.refine. The
script looks for isolated metals (not Fe in Heme, eg) and determines
the coordination sphere. The distance cutoff can be adjusted. The bond
lengths are taken from a lookup table while the angles are taken from
the input geometry. You should probably not include the angles when
the structure is not well refined so you can edit the "edits" or use
an option to phenix.metal_coordination.
Nigel
On Fri, Nov 4, 2011 at 9:06 AM, Laurie Betts <laurie.betts0508@gmail.com> wrote:
> How does PHENIX know where to look for proper bond lengths and angles for a
> metal ion I add to a protein structure - do I just add the metal into
> difference density and any waters, and then run ready set and it knows where
> to look for that particular metal and the atoms to which is is coordinated?
> And shouldn't there be a 'cif file that it outputs, or is that something
> that I need to get myself? Sorry it's still not obvious to me from the
> documentation.
>
> Thanks
>
> Laurie Betts
>
> _______________________________________________--
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb