[phenixbb] Refining an ion on a special position

Pavel Afonine pafonine at lbl.gov
Fri Jan 11 11:33:26 PST 2019

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 
> <http://www.phenix-online.org/pipermail/phenixbb/2018-February/023689.html>. 
> 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.


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