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Phenix.refine used to be able to handle a ligand covalently bound to cysteine if an appropriate cif dictionary was provided.
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<div class="">This now seems to be broken. Re-running a job that used to work now fails.</div>
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<div class=""><font face="Menlo" class="">KeyError : 'link_CYS-MPS'</font></div>
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<div class=""><font face="Menlo" class="">Traceback:</font></div>
<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 180, in run</font></div>
<div class=""><font face="Menlo" class=""> return_value = self.target()</font></div>
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<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 75, in __call__</font></div>
<div class=""><font face="Menlo" class=""> result = self.run()</font></div>
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</font></div>
<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 79, in run</font></div>
<div class=""><font face="Menlo" class=""> refine_object = self._run(args, callback)</font></div>
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<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 92, in _run</font></div>
<div class=""><font face="Menlo" class=""> call_back_handler=callback)</font></div>
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<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 106, in run</font></div>
<div class=""><font face="Menlo" class=""> log=log)</font></div>
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</font></div>
<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 224, in __init__</font></div>
<div class=""><font face="Menlo" class=""> run_clash_guard=False)</font></div>
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</font></div>
<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 1124, in setup_restraints_manager</font></div>
<div class=""><font face="Menlo" class=""> assume_hydrogens_all_missing = not self.has_hd())</font></div>
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<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5509, in geometry_restraints_manager</font></div>
<div class=""><font face="Menlo" class=""> log=self.log)</font></div>
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</font></div>
<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5154, in construct_geometry_restraints_manager</font></div>
<div class=""><font face="Menlo" class=""> log=log,</font></div>
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</font></div>
<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/linking_mixins.py", line 751, in process_nonbonded_for_links</font></div>
<div class=""><font face="Menlo" class=""> origin_id = origin_ids['link_%s' % key]</font></div>
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<div class=""><font face="Menlo" class=""> File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/cctbx/geometry_restraints/linking_class.py", line 35, in __getitem__</font></div>
<div class=""><font face="Menlo" class=""> raise e</font></div>
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