Dear CCP4BB
The PDB is introducing versioning of PDB entries.
As part of this work a new FTP
repository,ftp://ftp-versioned.wwpdb.org/now hosts versioned structural
model files in PDBx/mmCIF and PDBML formats.
Asannounced
<https://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8>on
May 17, 2017, wwPDB has introduced a versioning system to enable
depositor-initiated or wwPDB-initiated updates to previously released
PDB entries while retaining the same PDB accession code. Updates to
atomic coordinates, polymer sequence or chemical description in a PDB
coordinate file will trigger a major version increment. Other changes
will be classified as minor. All major versions of each PDB structure
are retained in the new FTP archive.
In the 2018 phase of the project, wwPDB will enable depositor-initiated
updates of coordinates.
File names in the versioned FTP archive conform to a new naming scheme,
which allows users to easily see the major and minor version numbers:
<PDB_ID>_<content_type>_v<major_version>-<minor_version>.<file_format_type>.<file_compression_type>
The familiar 4-character PDB accession code is extended to 8 characters
prefixed with “pdb”. Thus PDB accession code for entry 1abc becomes
pdb_00001abc. This new format of PDB accession code will be included in
the model files at a later date. For example, the first initial release
of PDB entry 1abc would have the following form under the new
file-naming scheme:
pdb_00001abc_xyz_v1-0.cif.gz
where xyz stands for coordinate content; cif indicates the file format;
and gz indicates a compressed UNIX archive file.
The first minor revision of PDB entry 1abc would then have the following
name:
pdb_00001abc_xyz_v1-1.cif.gz
If PDB entry 1abc then had a major update, it would have the following name:
pdb_00001abc_xyz_v2-0.cif.gz (N.B.: The minor update number will be
reset to zero every time a new major update is made.)
The versioned data files for a particular entry are stored in single
directory following a 2-character hash from the two penultimate
characters of the PDB code:
../pdb_versioned/data/entries/<two-letter-hash>/<pdb_accession_code>/<entry_data_File_names>
For example, major version 1 with minor version 2 file for entry 1ABC
would have the following path:
../pdb_versioned/data/entries/ab/pdb_00001abc/pdb_00001abc_xyz_v1-2.cif.gz
Different views of the repository are provided for content type and
format as a convenience for repository users. The wwPDB provides a link
to the absolutely latest version files as well as latest version of each
major version in the entries directories.
For example, users can access the absolute latest version of each
coordinate mmCIF file (e.g. 1ABC) via below file path.
../pdb_versioned/views/latest/coordinates/mmcif/ab/pdb_00001abc/pdb_00001abc_xyz.cif.gz
→../pdb_versioned/data/entries/ab/pdb_00001abc/pdb_00001abc_xyz_v2-0.cif.gz
Or users can access all major versions of coordinate mmCIF files for
entry 1ABC via below file path.
../pdb_versioned/views/all/coordinates/mmcif/ab/pdb_00001abc/pdb_00001abc_xyz_v1.cif.gz
→../pdb_versioned/data/entries/ab/pdb_00001abc/pdb_00001abc/pdb_00001abc_xyz_v1-2.cif.gz
../pdb_versioned/views/all/coordinates/mmcif/ab/pdb_00001abc/pdb_00001abc/pdb_00001abc_xyz_v2.cif.gz
→../pub/pdb_versioned/data/entries/ab/pdb_00001abc/pdb_00001abc_xyz_v2-0.cif.gz
Data files in the current archive location
ftp://ftp.wwpdb.org/pub/pdb/data/structures/ will continue to use the
familiar naming style and will continue to contain only the latest
version for every entry.
John
--
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529
http://www.pdbe.org
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