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<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I�ve noticed that command line phenix.model_vs_sequence does not work in phenix-1.21rc1-5156.
<o:p></o:p></span></span></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></span></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Here�s the data:<o:p></o:p></span></span></p>
<p class="p1"><span class="s1"><o:p> </o:p></span></p>
<p class="p1"><span class="s1">[tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence</span><o:p></o:p></p>
<p class="p1"><span class="s1">/linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence</span><o:p></o:p></p>
<p class="p1"><span class="s1">[tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb ../depo/8DKP.fasta</span><o:p></o:p></p>
<p class="p1"><span class="s1">Traceback (most recent call last):</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">File "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", line 75, in <module></span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">run(sys.argv[1:])</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">File "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py", line 48, in run</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">pdb_in = iotbx.pdb.inpu(params.input.pdb_file)</span><o:p></o:p></p>
<p class="p1"><span class="s1">AttributeError: 'module' object has no attribute 'inpu'</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">It worked fine in <span class="s1">phenix-1.20.1-4487</span>:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="p1"><span class="s1">[tannerjj@dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh</span><o:p></o:p></p>
<p class="p1"><span class="s1">[tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence</span><o:p></o:p></p>
<p class="p1"><span class="s1">/linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence</span><o:p></o:p></p>
<p class="p1"><span class="s1">[tannerjj@dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb ../depo/8DKP.fasta</span><o:p></o:p></p>
<p class="p1"><span class="s1">Skipping non-polymer chain 'A'</span><o:p></o:p></p>
<p class="p1"><span class="s1">Skipping non-polymer chain 'B'</span><o:p></o:p></p>
<p class="p1"><span class="s1">Skipping non-polymer chain 'A'</span><o:p></o:p></p>
<p class="p1"><span class="s1">Skipping non-polymer chain 'B'</span><o:p></o:p></p>
<p class="p1"><span class="s1">Chain 'A':</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">best matching sequence: 8DKP_1|Chains</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">sequence identity: 100.00%</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">10 residue(s) missing from PDB chain (3 at start, 1 at end)</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">1 gap(s) in chain</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">---QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||
</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">XGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||
</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">SGS---------------------------------------------------------</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space">
</span><span class="s1">|||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">---------------------------------------------MMGEQFVTGETIREA</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">DPKVSIDELIADPVEVV-</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">|||||||||||||||||
</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">DPKVSIDELIADPVEVVR</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">Chain 'B':</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">best matching sequence: 8DKP_1|Chains</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">sequence identity: 100.00%</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">8 residue(s) missing from PDB chain (0 at start, 1 at end)</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">1 gap(s) in chain</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">|||||||||||||||||||||||||||||||||||||||||||||||||||||||
</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">XXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">|
</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">SGS---------------------------------------------------------</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space">
</span><span class="s1">|||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">---------------------------------------------MMGEQFVTGETIREA</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">PDB file</span><span class="apple-converted-space">
</span><span class="s1">DPKVSIDELIADPVEVV-</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span class="s1">|||||||||||||||||
</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">sequence</span><span class="apple-converted-space">
</span><span class="s1">DPKVSIDELIADPVEVVR</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">[tannerjj@dizzy pdbs]$</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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