Failure to parse mmCIF files lacking _atom_site.pdbx_PDB_ins_code

[bioinsilico]

The mmCIF parser raises the error:

"/usr/local/lib/python3.11/site-packages/biotite/structure/io/pdbx/component.py", line 201, in __getitem__ element = self._elements[key] ~~~~~~~~~~~~~~^^^^^ KeyError: 'pdbx_PDB_ins_code'

when processing structure files that do not contain the _atom_site.pdbx_PDB_ins_code attribute. According to the mmCIF specification, this field may be absent or populated with "?" when no insertion code is defined. The current implementation appears to assume its presence unconditionally.

Some of the new IHM structures, such as 8ZZ4, 9A0P, 9A8I, ... don't include this item.

[padix-key]

Thanks for bringing this up. The required atom_site fields are more based on what PDBx files from PDB provide rather than what is really specified as mandatory column in the PDBx dictionary. Ideally get_structure should only depend on fields that are marked as 'Category key item' or 'Mandatory data item'.