[phenixbb] New bug in phenix.refine

[Aaron Oakley]

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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