<div dir="ltr">On Mon, Apr 21, 2014 at 6:41 PM, Chris Fage <span dir="ltr"><<a href="mailto:cdfage@gmail.com" target="_blank">cdfage@gmail.com</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><div><div><div><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></div>
<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>
</div></div></blockquote><div><br></div><div>Take a look at the first question in the "Models" section in our brand-new FAQ list:</div><div><br></div><div><a href="https://www.phenix-online.org/version_docs/1.9-1681/faqs/index.html#models">https://www.phenix-online.org/version_docs/1.9-1681/faqs/index.html#models</a><br>
</div><div><br></div><div>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.</div><div><br></div>
<div>That RuntimeError message really does sound like a bug; I'll investigate soon.</div><div><br></div><div>-Nat</div></div></div></div>