Re: [phenixbb] metal coordination restraints

Thanks for the friendly help for the sometimes clueless! It's working. On Fri, Nov 4, 2011 at 12:49 PM, Nigel Moriarty 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 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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