[3dem] Distributing PDBx/mmCIF-Formatted Assembly Files
Justin Flatt
justin at rcsb.rutgers.edu
Thu May 5 05:46:45 PDT 2022
Starting May 3, 2022, the PDB archive distributes assembly files in
PDBx/mmCIF format, allowing direct access and visualization of the
curated assemblies for all PDB entries
(http://www.wwpdb.org/news/news?year=2022#61f7f8bc8f40f9265109d398).
Previously, PDBx/mmCIF formatted assembly files provided for structures
were 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 led 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 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 are provided:
_pdbx_entity_remapping and _pdbx_chain_remapping.
A new directory (https://ftp.wwpdb.org/pub/pdb/data/assemblies/) was
created for the distribution of these updated assembly files. The
directory containing the existing assembly mmCIF files for large entries
has been 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 were
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=cOM-WPmahdrUaPhXqRn2gInq0xZzh2aqymry8dX94cC5xBX-c2SZvzy2eYCiSX_0&s=irfSN4ACaC_iGGTrBxUw-FutMNLZPc9BwU66m_K3iCs&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), for improved efficiency.
For any further information please email info at wwpdb.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20220505/58a0fedb/attachment.html>
More information about the 3dem
mailing list