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<body class='hmmessage'><div dir='ltr'>Dear Nat,<div><br></div><div>You are right. </div><div><br></div><div>I added two metal ions Zn and Mg and after that I started getting this error.</div><div><br></div><div>I did run <span style="font-size: 12pt;">phenix.metal_coordination to get elbow.edits and add this to refinement to to get same error. </span></div><div><span style="font-size: 12pt;"><br></span></div><div><span style="font-size: 12pt;">I am not running with water update option.</span></div><div><span style="font-size: 12pt;"><br></span></div><div>I ran the pdb through readyset and added metal restraints, processed pdb file and ligand restraints to the refinement to get same error.</div><div><br></div><div>The Zinc and Mg are not coordinated well. I have added because nothing fits in the density. I am not sure lack coordination is creating the problem. I will send ATOM records to Pavel.</div><div><br></div><div>Thanks a lot for looking in to this one.</div><div><br></div><div>SDY<br><br><div><hr id="stopSpelling">From: nechols@lbl.gov<br>Date: Tue, 4 Mar 2014 07:50:31 -0800<br>Subject: Re: [phenixbb] phenix error<br>To: ccp4_sc@hotmail.com<br>CC: phenixbb@phenix-online.org<br><br><div dir="ltr">You probably have metal coordination restraints that are no longer valid - each time you run phenix.refine with the solvent update enabled, the numbering of waters will change and the old restraints become invalid. �The utilities menu in the phenix.refine GUI has an option to clear these out entirely; you can then run ReadySet again to generate new restraints.<div>
<br></div><div>-Nat</div></div><div class="ecxgmail_extra"><br><br><div class="ecxgmail_quote">On Mon, Mar 3, 2014 at 10:31 PM, SD Y <span dir="ltr"><<a href="mailto:ccp4_sc@hotmail.com" target="_blank">ccp4_sc@hotmail.com</a>></span> wrote:<br>
<blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">Hi,<div><br></div><div>Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69".�</div><div><br></div><div>Log file ends as follows:</div>
<div><br></div><div><div>============================= Scattering factors =============================</div><div><br></div><div><br></div><div>� � � � � � � � ----------X-ray scattering dictionary---------- � � � � � � � �</div>
<div><br></div><div>Number of scattering types: 7</div><div>� Type �Number � �sf(0) � Gaussians</div><div>� �Zn2+ � � 1 � � 27.88 � � � 1</div><div>� �S � � � 10 � � 15.96 � � � 2</div><div>� �P � � � �2 � � 14.95 � � � 2</div>
<div>� �Mg2+ � � 3 � � �9.96 � � � 1</div><div>� �O � � �635 � � �7.97 � � � 2</div><div>� �N � � �523 � � �6.97 � � � 2</div><div>� �C � � 1983 � � �5.97 � � � 2</div><div>� sf(0) = scattering factor at diffraction angle 0.</div>
<div><br></div><div><br></div><div>========================== Anomalous scatterer groups =========================</div><div><br></div><div>All atoms refined with f_prime=0 and f_double_prime=0.</div><div><br></div><div>
======================== Summary of geometry restraints =======================</div>
<div><br></div><div>� Number of disulfides: simple=0, symmetry=0</div><div>� Custom bonds:</div><div>Sorry</div></div><div>------------------------------</div><div><br></div><div>Thanks a lot</div><div>SDY</div> </div>
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