[phenixbb] metal ions in phenix.ensemble_refinement

Lance Westerhoff lance at quantumbioinc.com
Sun Feb 9 08:46:39 PST 2014

Hi Scott-

You are welcome to try out our plugin to phenix. As detailed in the recent Phenix newsletter, this tool uses a fast QM calculation within the active site and can capture the chemistry between the ligand, the Zn, and the surrounding residues. You do not need to define a prior restraints for the coordination sphere. For more information take a look at this link:


We have run several Zn systems. The following case study for example shows the importance of protonation and electrostatics in the active site and how these can influence refinement.


Let me know if you have any questions!

Lance M. Westerhoff, Ph.D.
President and General Manager
QuantumBio Inc. 

WWW:    http://www.quantumbioinc.com

On Feb 7, 2014, at 9:04 AM, Scott Horowitz wrote:

> 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!
> Thanks,
> Scott
> -- 
> 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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