[phenixbb] Refining an ion on a special position
pafonine at lbl.gov
Fri Jan 11 11:33:26 PST 2019
> 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
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.
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.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb