[phenixbb] Refining an ion on a special position

Shane Caldwell shane.caldwell17 at gmail.com
Fri Jan 11 13:21:19 PST 2019


Aha - looks like this works! I set the occupancy to 1.0 and the relevant
coordinates to 0.0 and phenix.refine does the right thing. I guess this
just doesn't happen if occupancy is less than 1 (or maybe coordinates need
to be precisely on-axis?)

Thanks, Paul and Pavel!

Shane Caldwell
shane.caldwell17 at gmail.com


On Fri, Jan 11, 2019 at 11:44 AM Paul Adams <pdadams at lbl.gov> wrote:

>
> Maybe something has changed, but originally phenix.refine would
> automatically determine if an atom was on a special position, adjust the
> occupancy accordingly, and keep the ion on the axis during refinement.
> There was no requirement to set the occupancy to something other than 1,
> nor turn off symmetry interactions. What happens if you give the ion an
> occupancy of 1 and leave the symmetry interactions as normal?
>
>
> > On Jan 11, 2019, at 11:33 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> >
> > Hi Shane,
> >
> >> I've got a question related to refinement of an ion on a special
> position. I have a structure with an atom placed squarely on the C2 axis.
> I've been able to get a mostly-reasonable model by dropping in the ion at
> 0.5 occupancy and turning off repulsion for the ion in question, as Pavel
> describes here. It almost completely works.
> >
> > OK, all sounds good so far!
> >
> >> The thing I find now is that during refinement there can still be some
> random drift of the atom away from the symmetry axis, splitting from its
> symmetry ghost, while I know that it should stay perfectly coincident.
> >
> > Hm.. this is odd and I'm pretty sure the code that handles this makes
> sure atoms on special position should stay there perfectly (no drifting).
> >
> >> My resolution is 3.1 and there's no indication of a multiple
> conformation, so a split isn't justified. The most parsimonious model
> should place the ion exactly on the C2.
> >
> > All true!
> >
> > Looks like I need to investigate this in greater detail.. Would it be
> possible to send me model and data files, as well as any ligand cif (if
> used) and that will be a good start for me. I'm traveling next week, so if
> I get files today I may be able to respond before my travels.
> >
> > Pavel
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: phenixbb-leave at phenix-online.org
>
> --
> Paul Adams
> Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence
> Berkeley Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley
> Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Laboratory Research Manager, ENIGMA Science Focus Area
>
> Building 33, Room 347
> Building 978, Room 4126
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 33R0345
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][
> 1-510-495-2506 ]
> --
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190111/b7760675/attachment.htm>


More information about the phenixbb mailing list