Hi everyone,<div><br></div><div>I am getting following error while running phenix refinement for a protein cocrystalized with a metal chelator complex. What could be the problem.</div><div><br></div><div>
<p class="MsoNormal"><span style="font-family:Courier">AssertionError : </span></p>
<p class="MsoNormal"><span style="font-family:Courier">Traceback:</span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File
"/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/thread_utils.py",
line 229, in run</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> return_value = self._target(self._args,
self._kwargs, self._c)</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File
"/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/libtbx/runtime_utils.py",
line 72, in __call__</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> result = self.target()</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File
"/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/runtime.py",
line 67, in __call__</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> call_back_handler=callback)</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File
"/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py",
line 97, in run</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> call_back_handler=call_back_handler)</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File "/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/driver.py",
line 1478, in run</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> ncs_manager
= self.ncs_manager)</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File
"/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/phenix/phenix/refinement/strategies.py",
line 344, in refinement_machine</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> model.show_occupancy_statistics(text =
"Occupancies statistics", out=log)</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File
"/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/mmtbx/model.py",
line 868, in show_occupancy_statistics</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> self.xray_structure.set_occupancies(value=0.,
selection = less_than_zero)</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"><span style="font-family:Courier">
File
"/Applications/PHENIX-1.7.3-928/Contents/phenix-1.7.3-928/cctbx_project/cctbx/xray/structure.py",
line 480, in set_occupancies</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> assert selection.size() == s.size()</span></p>
<p class="MsoNormal"><span style="font-family:Courier"> </span></p>
<p class="MsoNormal"> Thanks</p><p class="MsoNormal">Subhani</p>
</div>