Limitations

By design the library maps the PDBx/ModelCIF data model to its own hierarchy of Python objects. This hierarchy does not cover every possible mmCIF category; thus, the library is not necessarily preserving of file contents (e.g. if a file is read in and then a new file is written out, categories or data items from the original file not understood by the library will be missing in the new file).

In particular, many PDBx categories pertaining to experimentally-determined structures are ignored. Also, the following ModelCIF categories are currently not supported:

• ma_template_customized

• ma_template_coord

• ma_coevolution_seq_db_ref

• ma_coevolution_msa

• ma_coevolution_msa_details

• ma_restraints

• ma_distance_restraints

• ma_angle_restraints

• ma_dihedral_restraints

• ma_restraints_group

• ma_poly_template_library_details

• ma_poly_template_library_list

• ma_poly_template_library_components

Note that currently the library is only well-tested with single-chain homology models generated from a single template (such as those in the ModBase database).

Please open an issue if library support is lacking.