arpeggio fails on some PDB structures

[avivrosenberg]

There are PDB structures on which arpeggio fails.

For example on 6S2M and 5NW3, the following error is produced:

Traceback (most recent call last):
  File "/Users/avivr/mambaforge/envs/arpeggio/bin/arpeggio", line 8, in <module>
    sys.exit(main())
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/scripts/process_protein_cli.py", line 79, in main
    run_arpeggio(args)
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/scripts/process_protein_cli.py", line 103, in run_arpeggio
    i_complex.initialize()
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 318, in initialize
    self._add_atomic_radii()
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 1493, in _add_atomic_radii
    atom.vdw_radius = ob.etab.GetVdwRad(self.ob_mol.GetAtomById(self.bio_to_ob[atom]).GetAtomicNum())
AttributeError: 'NoneType' object has no attribute 'GetAtomicNum'

On 1IX9, a different error:

Traceback (most recent call last):
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 1995, in _establish_structure_mappping
    biopython_atom = serial_to_bio[serial]
KeyError: 3478

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/avivr/mambaforge/envs/arpeggio/bin/arpeggio", line 8, in <module>
    sys.exit(main())
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/scripts/process_protein_cli.py", line 79, in main
    run_arpeggio(args)
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/scripts/process_protein_cli.py", line 89, in run_arpeggio
    i_complex = InteractionComplex(args.filename, args.vdw_comp, args.interacting, args.ph)
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 92, in __init__
    self._establish_structure_mappping()
  File "/Users/avivr/mambaforge/envs/arpeggio/lib/python3.7/site-packages/arpeggio/core/interactions.py", line 1998, in _establish_structure_mappping
    raise OBBioMatchError(serial)
arpeggio.core.exceptions.OBBioMatchError: 3478

In these examples, I was running e.g. arpeggio -o out/arpeggio -s /A// -i 4.5 data/pdb/1ix9.cif, but it doesn't seem to be affected by the selection or the cutoff argument.

Are these known issues? is there any way to work around them?

Thanks.