This now seems to be broken. Re-running a job that
used to work now fails.
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