<div dir="ltr"><div>Hi ,</div><div>I am trying to fix a  pdb file that was obtained from Rosetta and has some distorted helices</div><div>so I trier to fix that with <br></div><div><br></div><div>&gt; phenix.model_idealization model.pdb <span class="gmail-phil-name">use_ss_restraints</span><span class="gmail-phil-words"> = True <br></span></div><div><span class="gmail-phil-words"><br></span></div><div><span class="gmail-phil-words">I am attaching the log file ,  here is the end of the log file. Any suggestions on what&#39;s going on ?<br></span></div><div><span class="gmail-phil-words"><br></span></div><div>&quot; NOTE: a complete listing of the restraints can be obtained by requesting<br>        output of .geo file.<br>Traceback (most recent call last):<br>  File &quot;/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py&quot;, line 1118, in &lt;module&gt;<br>    run(sys.argv[1:])<br>  File &quot;/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py&quot;, line 1106, in run<br>    mi_object.run()<br>  File &quot;/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py&quot;, line 548, in run<br>    self._setup_model_h()<br>  File &quot;/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py&quot;, line 478, in _setup_model_h<br>    params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation<br>AttributeError: &#39;NoneType&#39; object has no attribute &#39;pdb_interpretation&#39;&quot;<br></div><div><span class="gmail-phil-words"><br></span></div><div><span class="gmail-phil-words"><br></span></div><div><span class="gmail-phil-words">My aim is to idealize the secondary structure. I first tried it in Isolde but the</span></div><div><span class="gmail-phil-words">EM density is not great and always leads to some distortion. So I was wondering if I can do this fix</span></div><div><span class="gmail-phil-words">in Phenix.  Is this model idealization tool the best approach?  or I have to go in and fix things manually.</span></div><div><span class="gmail-phil-words"><br></span></div><div><span class="gmail-phil-words">Thanks</span></div><div><span class="gmail-phil-words">Manoj<br></span></div></div>