[phenixbb] refining the anomalous Se in MSE using Phenix Gui

Nathaniel Echols nechols at lbl.gov
Thu Jun 27 13:55:24 PDT 2013

On Thu, Jun 27, 2013 at 1:32 PM, Kenneth A. Satyshur <satyshur at wisc.edu> wrote:
> I am trying to refine the anomalous data in phenix refine. I am using the GUI and I get a box for
> the anomalous groups. But I when I put in 'Se' and refine: phenix says 'Sorry'. If I use View, I get all atoms in a viewer. I have
> 5 molecules of 330 residues each and 25 total Se atoms. I cannot possibly pick them out from the molecular
> display. Then I tried to make a heavy atom file with just selenium in it, but on input, it is read as a 'input model' and
> when I refine, it says 'duplicate atoms'. Without the anomalous refine, there is a lot of residual Fo-Fc density around the
> seleniums in the maps.
> How do I enter the 'anomalous group' into phenix refine. What is the syntax? I can find no help file or documentation
> on this. Anyone done this before?

"element Se"

more examples here:

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