[phenixbb] metal coordination restraints

Nigel Moriarty nwmoriarty at lbl.gov
Fri Nov 4 09:49:02 PDT 2011


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.


On Fri, Nov 4, 2011 at 9:06 AM, Laurie Betts <laurie.betts0508 at 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
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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