Re: [phenixbb] Trouble Refining Ligand in Phenix

Based on the information available at Nat's link, I manually reset the occupancies of the problematic atoms in the PDB to unity. This solved my problem. Thanks! Chris On 4/21/14, Nathaniel Echols wrote:

On Mon, Apr 21, 2014 at 6:41 PM, Chris Fage wrote:

...

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: "refine_65-coot-2.metal.edits" 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.

Take a look at the first question in the "Models" section in our brand-new FAQ list:

https://www.phenix-online.org/version_docs/1.9-1681/faqs/index.html#models

If these suggestions don't fix the problem, it could be a bug, in which case we'd like to see the inputs - but the Phaser behavior is usually the correct explanation.

That RuntimeError message really does sound like a bug; I'll investigate soon.

-Nat