[phenixbb] metal ions in phenix.ensemble_refinement

[Scott Horowitz]

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?

Thanks,
Scott


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:
>
>         http://www.quantumbioinc.com/products/phenix_divcon
>
> 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.
>
>         http://www.quantumbioinc.com/publications/show/CS-Xray_1AZM
>
> Let me know if you have any questions!
>
> -Lance
> ____________________
> 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
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
>
>
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>



-- 
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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