[phenixbb] Trouble Refining Ligand in Phenix

Chris Fage cdfage at gmail.com
Mon Apr 21 18:41:09 PDT 2014

Hi Everyone,

I am trying to refine a structure with a phosphorylated amino acid. After
refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density
for all atoms of the derivatized amino acid in Coot, almost as if I had not
built in the residue. I am loading a .cif for the derivative when I run
phenix.refine. I have also tried ReadySet, but when I click the "Run in
phenix.refine" button, I see the message

Error interpreting command line argument as parameter definition:
RuntimeError: Unexpected end of output.

Am I just seeing noise, or is Phenix not actually refining this portion of
the model? I would appreciate any suggestions.

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