[phenixbb] metal ions in phenix.ensemble_refinement

Scott Horowitz horowsah at umich.edu
Fri Feb 7 06:04:38 PST 2014

Hi, I'm trying to use phenix.ensemble_refinement, and my structure has
several zinc atoms, both coordinated to amino acids and free imidazoles,
and sometimes both. It looks as though it's not really understanding that
the zincs really should stay more or less in their coordination spots, and
are spending some time in kind of weird spots. I couldn't find anything
documented that seems like it will help, unless there's some clever way to
use the harmonic restraints for this that I haven't figured out.

And while I'm at it, I have another potentially related problem: the rfree
of my final ensemble (0.27) is substantially higher than my input structure
(0.24). And yes, I had been doing my refinement in phenix, with hydrogens
added, and I optimized pTLS. If you're curious, this is a 1.9 A structure.

Any help and/or suggestions would be greatly appreciated!


Scott Horowitz, Ph.D.
Research Associate
Howard Hughes Medical Institute

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226
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