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

Emilia C. Arturo (Emily) eca38 at drexel.edu
Thu May 21 12:22:56 PDT 2015

> A more recent survey could possibly be of help to you

Yes, I'd been looking at Zheng et al's 2008 paper
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872550/> reporting the
NEIGHBORHOOD database, and the Fe-ligand distances that I observe in my
structure are significantly outside of this range (by up to ~35%). I'm
going to further into this and maybe pose the question to a broader
audience at some point.

> 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.

Ah! I hadn't known about the slack parameter; now I know (this is now
Thanks to you both!


> Cheers
> Nigel
> ---
> 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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