<div dir="ltr">Hi Philippe,<div><br></div><div>Thank you for reporting the issue. Can you please send me (OFF list) the file you used as input so I can fix the issue? All files sent to me are treated as confidential.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, May 5, 2023 at 2:02 AM CUNIASSE Philippe <<a href="mailto:Philippe.CUNIASSE@cea.fr">Philippe.CUNIASSE@cea.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg-5539976624555181817">
<div lang="FR" style="overflow-wrap: break-word;">
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<p class="MsoNormal"><span lang="EN-US" style="font-size:14pt;color:black">Dear all,<span class="m_-5539976624555181817apple-converted-space"> </span></span><span lang="EN-US" style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="font-variant-caps:normal;text-align:start;word-spacing:0px">
<span lang="EN-US" style="font-size:14pt;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" target="_blank"><span style="font-size:11pt;color:rgb(5,99,193)">https://phenix-online.org/documentation/reference/model_idealization.html</span></a></span><span lang="EN-US" style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="font-variant-caps:normal;text-align:start;word-spacing:0px">
<span lang="EN-US" style="font-size:14pt;color:black">phenix.model_idealization xxxx.pdb</span><span lang="EN-US" style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="font-variant-caps:normal;text-align:start;word-spacing:0px">
<span lang="EN-US" style="font-size:14pt;color:black">But the code stops on the error :</span><span lang="EN-US" style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal" style="font-variant-caps:normal;text-align:start;word-spacing:0px">
<span lang="EN-US" style="font-size:14pt;color:black"> </span><span lang="EN-US" style="color:black"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817apple-converted-space"><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"> </span></span><span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span class="m_-5539976624555181817s1"><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"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span lang="EN-US" style="font-size:14pt">Thanks in advance for any suggestion to solve this.</span><span lang="EN-US" style="font-size:10.5pt;font-family:Courier;color:black"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span style="font-size:14pt">Best regards.</span><span style="font-size:10.5pt;font-family:Courier;color:black"><u></u><u></u></span></p>
<p class="m_-5539976624555181817p1" style="margin:0cm;font-variant-caps:normal;text-align:start;word-spacing:0px">
<span style="font-size:14pt">Philippe.</span><span style="font-size:10.5pt;font-family:Courier;color:black"><u></u><u></u></span></p>
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<span lang="EN-US" style="font-size:14pt;color:black"> </span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:14pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">-----------------------------------------------</span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Philippe Cuniasse, PhD/HDR.</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Institut de Biologie Integrative de la cellule.</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">UMR 9198 CNRS-CEA-Univ Paris Sud</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Bat 144 CE-Saclay</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">91191 Gif-sur-Yvette Cedex</span><span style="font-size:13.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9pt;font-family:Courier;color:black">France</span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9pt;font-family:Courier;color:black">Tel: (33) 1 69 08 56 35</span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Fax: (33) 1 69 08 47 12</span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Email: </span><span style="font-size:9pt;font-family:Courier;color:rgb(0,0,254)"><a href="mailto:philippe.cuniasse@cea.fr" target="_blank"><span style="color:purple">philippe.cuniasse@cea.fr</span></a></span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:9pt;font-family:Courier;color:black">Web:</span><span style="font-size:9pt;font-family:Courier;color:rgb(0,0,245)"> <a href="http://biodev.cea.fr/rasmot3d/" target="_blank"><span style="color:purple">http://biodev.cea.fr/rasmot3d/</span></a></span><span style="font-size:10.5pt;color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><i><span style="font-size:10pt;font-family:"Times New Roman",serif;color:black"><img border="0" id="m_-5539976624555181817Image_x0020_3" src="cid:188212b9a7f4cff311" alt="signature_3031510868"></span></i></b><span style="font-size:12pt;font-family:"Comic Sans MS";color:black"><img border="0" id="m_-5539976624555181817Image_x0020_2" src="cid:188212b9a805b16b22" alt="signature_394100311"><img border="0" id="m_-5539976624555181817Image_x0020_1" src="cid:188212b9a80692e333" alt="signature_2972121752"><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:14pt"><u></u> <u></u></span></p>
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