[phenixbb] metal coordination restraints

Laurie Betts laurie.betts0508 at gmail.com
Fri Nov 4 10:14:36 PDT 2011


Thanks for the friendly help for the sometimes clueless!  It's working.

On Fri, Nov 4, 2011 at 12:49 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> 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 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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> > phenixbb at 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 at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
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