Dear ccp4bb,
Starting May 3rd 2022, the PDB archive will distribute assembly files in
PDBx/mmCIF format, allowing direct access and visualisation 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,
standardised 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:
o
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.)
o
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,
_pdbx_entity_remapping and _pdbx_chain_remapping will be provided.
A new directory, https://ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/
<https://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 (https://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
https://github.com
<https://github.com/wwpdb/assembly-mmcif-examples>/wwpdb/assembly-mmcif-examples
<http://github.com/wwpdb/assembly-mmcif-examples>.
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 i...@wwpdb.org.
<mailto:i...@wwpdb.org>
Kind Regards,
David Armstrong
--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544
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