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<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">Hello all,</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">I am trying to use the command line tool phenix.sculpt_ensemble to process a series of PDB files in preparation for molecular replacement.</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">However, when I run the following on the command line:</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none">phenix.sculpt_ensemble 2*.pdb input.target_sequence=RRAS2.fasta<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">I get the following errors:</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none"> File "/Applications/phenix-1.21rc1-5015/build/../modules/phaser/phaser/command_line/sculpt_ensemble.py", line 84, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none"> sculpt_ensemble.run( phil = params.phil, logger = logger )<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none"> File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 610, in run<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none"> logger = logger,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none"> File "/Applications/phenix-1.21rc1-5015/modules/phaser/phaser/sculpt_ensemble.py", line 259, in read_in_target_sequence_files<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none"> for ( fname, i ) in itertools.zip_longest( filenames, range( 1, nchains + 1 ) ):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:Menlo;color:black;mso-ligatures:none">AttributeError: 'module' object has no attribute 'zip_longest'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">I am running phenix 1.21rc1-5015-000 on Mac OS 13.5.1.</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">Any ideas?</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none"> </span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">Thanks,</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Grandview",sans-serif;color:#212121;mso-ligatures:none">Matthew</span><span style="color:#212121;mso-ligatures:none"><o:p></o:p></span></p>
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