[phenixbb] where do phenix.metal_coordination ideal bond lengths come from?

Nigel Moriarty nwmoriarty at lbl.gov
Fri May 14 08:29:41 PDT 2010


The primary sources are

Acta Cryst. D62 (2006), 678-682
J. Comput. Chem. 14, (1993), 961-969
Journal of Inorganic Biochemistry 102 (2008) 1765–1776

You can easily edit the output file to change the values or set
use_default_bondlengths=False (older version have this as the default)
to use the input geometry as the guide.


On Thu, May 13, 2010 at 10:16 PM, Scott Classen <sclassen at lbl.gov> wrote:
> Hello,
> I have a structure with several water/carboxylate-coordinated metal ions and I am using phenix.metal_coordination to generate the restraints parameter file for phenix.refine. Can someone please tell me where phenix.metal_coordination is getting the ideal bond length/angle values from.
> Thanks,
> Scott Classen
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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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