Hi Aaron, could you please send us relevant files and tell the steps that lead to this crash (we need to reproduce this first before we can comment)? Thanks, Pavel On 6/21/19 04:05, Aaron Oakley wrote:
Phenix.refine used to be able to handle a ligand covalently bound to cysteine if an appropriate cif dictionary was provided.
This now seems to be broken. Re-running a job that used to work now fails.
KeyError : 'link_CYS-MPS' Traceback: File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 180, in run return_value = self.target()
File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 75, in __call__ result = self.run()
File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 79, in run refine_object = self._run(args, callback)
File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 92, in _run call_back_handler=callback)
File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 106, in run log=log)
File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 224, in __init__ run_clash_guard=False)
File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 1124, in setup_restraints_manager assume_hydrogens_all_missing = not self.has_hd())
File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5509, in geometry_restraints_manager log=self.log)
File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5154, in construct_geometry_restraints_manager log=log,
File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/linking_mixins.py", line 751, in process_nonbonded_for_links origin_id = origin_ids['link_%s' % key]
File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/cctbx/geometry_restraints/linking_class.py", line 35, in __getitem__ raise e
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