[phenixbb] metal ions in phenix.ensemble_refinement
horowsah at umich.edu
Mon Feb 10 05:45:58 PST 2014
Cool! I'll have to try that, I think. I'm curious about the choice of
semi-empirical vs. DFT; is DFT still too slow to work in most cases?
On Sun, Feb 9, 2014 at 11:46 AM, Lance Westerhoff
<lance at quantumbioinc.com>wrote:
> 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
> > 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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> > phenixbb at phenix-online.org
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Scott Horowitz, Ph.D.
Howard Hughes Medical Institute
University of Michigan
Department of Molecular, Cellular, and Developmental Biology
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
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