[phenixbb] metal-ligand distances, and Optimize X-ray/stereochemistry weights

Nigel Moriarty nwmoriarty at lbl.gov
Thu May 21 11:41:15 PDT 2015

On Thu, May 21, 2015 at 11:10 AM, Emilia C. Arturo (Emily) <eca38 at drexel.edu
> wrote:

> Yes, you're absolutely right, and I hadn't found documentation for
> phenix.metal_coordination to help me gauge whether 'my' irons were like
> those used to inform how phenix generated the edits file. Do you happen to
> know on what the tool bases its ideal distances?

There are taken from a literature survey some time ago.

> Do you have any references you can share that discuss how Fe-ligand
> distances change with charge and spin state, whether its observable in
> crystal structures or solution? Or, maybe you can suggest search terms to
> help me out as I am quite naive about bio-inorganic chemistry?

A more recent survey could possibly be of help to you but you have data
that may be telling you what you need to do. You can also add a slack
option to the edit which makes the potential well flat bottomed. If you
made it say 0.2 then the metal coordinate would be very flexible and you
wouldn't have the nonbonded term pushing them apart.



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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