[3dem] Distributing PDBx/mmCIF-Formatted Assembly Files

[Justin Flatt]

Dear PDB users,

Starting May 3, 2022, the PDB archive will distribute assembly files in 
PDBx/mmCIF format, allowing direct access and visualization of the 
curated assemblies for all PDB entries.

Currently, PDBx/mmCIF formatted assembly files are provided for 
structures that are non-PDB compliant, however the coordinates use model 
numbers to differentiate alternate symmetry copies of PDB chain IDs. 
This method is not ideal, nor necessary, for the current archive 
PDBx/mmCIF format and has lead to limited use of these files in 
community software tools. In response to this issue and recommendations 
by the wwPDB advisory committee, we are implementing updated, 
standardized practices for generation of assembly files 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:

# Chain IDs of the original chains from the atomic coordinate file will 
be retained (e.g., A)
# 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:

  * 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.)
  * 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.)

In addition, entity ID and chain ID mapping categories will be provided: 
_pdbx_entity_remapping and _pdbx_chain_remapping.

A new directory (ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/) will be 
created for the distribution of these updated assembly files. The 
directory containing the existing assembly mmCIF files for large entries 
will be removed (ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/ 
<https://ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/>).

wwPDB asks all PDB users and software developers to review code and 
address any limitations related to PDB assemblies. Sample files are made 
available for testing purposes and to support community adoption at 
GitHub.com/wwpdb/assembly-mmcif-examples 
(https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_wwpdb_assembly-2Dmmcif-2Dexamples&d=DwICAg&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=2HysGtd8GZeRbX9ZoRI-BVMoEMdt-1g2Qn7eixIhUAij7euIqh0T7kUWdidi9wpt&s=1UOj4lqZuRbuuZrJRJYm30fLK5138Pk-AE0EDHwGeVQ&e= ).

If you plan to use these assembly files for graphical viewing, check if 
your visualization software (e.g., PyMol, ChimeraX, etc.) supports 
instantiation of assemblies directly from atomic coordinate files 
(_struct_assembly related categories), you do so for improved 
efficiency.

For any further information please email info at wwpdb.org.
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