<div dir="ltr"><div><div><div><div>Hi Everyone,<br><br></div>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<br>
<br></div>Error interpreting command line argument as parameter definition:<br></div>"refine_65-coot-2.metal.edits"<br></div>RuntimeError: Unexpected end of output.<br><div><br>Am I just seeing noise, or is Phenix not actually refining this portion of the model? I would appreciate any suggestions.<br>
<br></div>Best,<br>Chris</div>