Starting May 3rd 2022, the PDB archive will distribute assembly files in PDBx/mmCIF format for every entry, allowing direct access and visualisation of the curated assemblies for all PDB entries.
These updated PDBx/mmCIF format assembly files will have improved organization of assembly data to support usage by the community. These files will include all symmetry generated copies of each chain within a single model, with distinct chain IDs (_atom_site.auth_asym_id and _atom_site.label_asym_id) assigned to each. Generation of distinct chain IDs in assembly files are based upon the following rules:
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Chain IDs of the original chains from the atomic coordinate file will be retained (e.g., A)
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Assign unique chain ID (atom_site.label_asym_id and atom_site.auth_asym_id) for each symmetry copy within a single model. Rules of chain ID assignments:
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The applied index of the symmetry operator (pdbx_struct_oper_list.id) will be appended to the original chain ID separated by a dash (e.g., A-2, A-3, etc.)
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If there are more than one type of symmetry operators applied to generate symmetry copy, a dash sign will be used between two operators (e.g., A-12-60, A-60-88, etc.)
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In addition, entity ID and chain ID mapping categories, _pdbx_entity_remapping and _pdbx_chain_remapping will be provided.
Within this repository are sample files. In May, the assembly files for the entire PDB archive will be available to the public under a new directory https://ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF.