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<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt;color:black">Dear all,<span class="apple-converted-space"> </span></span><span lang="EN-US" style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span lang="EN-US" style="font-size:14.0pt;color:black">I tried to use the phenix.model_idealization code of phenix (in command line) following the syntax suggested in<a href="https://phenix-online.org/documentation/reference/model_idealization.html" title="https://phenix-online.org/documentation/reference/model_idealization.html"><span style="font-size:11.0pt;color:#0563C1">https://phenix-online.org/documentation/reference/model_idealization.html</span></a></span><span lang="EN-US" style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span lang="EN-US" style="font-size:14.0pt;color:black">phenix.model_idealization xxxx.pdb</span><span lang="EN-US" style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span lang="EN-US" style="font-size:14.0pt;color:black">But the code stops on the error :</span><span lang="EN-US" style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span lang="EN-US" style="font-size:14.0pt;color:black"> </span><span lang="EN-US" style="color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">Traceback (most recent call last):</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 1118, in <module></span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">run(sys.argv[1:])</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 1106, in run</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">mi_object.run()</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 548, in run</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">self._setup_model_h()</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py",
line 478, in _setup_model_h</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black">AttributeError: 'NoneType' object has no attribute 'pdb_interpretation'</span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span class="s1"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span lang="EN-US" style="font-size:14.0pt">Thanks in advance for any suggestion to solve this.</span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:14.0pt">Best regards.</span><span style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
<p class="p1" style="margin:0cm;font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:14.0pt">Philippe.</span><span style="font-size:10.5pt;font-family:Courier;color:black"><o:p></o:p></span></p>
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<span lang="EN-US" style="font-size:14.0pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Philippe Cuniasse, PhD/HDR.</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Institut de Biologie Integrative de la cellule.</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">UMR 9198 CNRS-CEA-Univ Paris Sud</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Bat 144 CE-Saclay</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">91191 Gif-sur-Yvette Cedex</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">France</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Tel: (33) 1 69 08 56 35</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Fax: (33) 1 69 08 47 12</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Email: </span><span style="font-size:9.0pt;font-family:Courier;color:#0000FE;mso-fareast-language:FR"><a href="mailto:philippe.cuniasse@cea.fr"><span style="color:purple">philippe.cuniasse@cea.fr</span></a></span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Web:</span><span style="font-size:9.0pt;font-family:Courier;color:#0000F5;mso-fareast-language:FR"> <a href="http://biodev.cea.fr/rasmot3d/"><span style="color:purple">http://biodev.cea.fr/rasmot3d/</span></a></span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:FR"><img border="0" id="Image_x0020_3" src="cid:image001.png@01D97F40.8E5D3D50" alt="signature_3031510868"></span></i></b><span style="font-size:12.0pt;font-family:"Comic Sans MS";color:black;mso-fareast-language:FR"><img border="0" id="Image_x0020_2" src="cid:image002.png@01D97F40.8E5D3D50" alt="signature_394100311"><img border="0" id="Image_x0020_1" src="cid:image003.png@01D97F40.8E5D3D50" alt="signature_2972121752"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span style="font-size:14.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:14.0pt"><o:p> </o:p></span></p>
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