[phenixbb] New bug in phenix.refine

[Pavel Afonine]

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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