As announced
<https://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8> on
May 17, 2017, wwPDB will introduce a file versioning system to retain
depositor-initiated updates of previously released coordinate entries. A
new FTP repository will host versioned files. Versions will be separated
into major and minor updates. 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
latest major versions of each PDB structure will be retained in the new
FTP archive.
wwPDB will deliver versioned files in two phases:
* Phase 1 (October 2017), we will release the new versioned FTP
archive at ftp://ftp-version.wwpdb.org for structural model files in
PDBx/mmCIF and PDBML formats.
* Phase 2 will be released in 2018 and will support
depositor-initiated updates of coordinates in PDBx/mmCIF and PDBML
formats.
File names in the versioned FTP archive will conform to a new naming
scheme, which allows users to easily see the major and minor version number:
<PDB_ID>_<content_type>_v<major_version>-<minor_version>.<file_format_type>.<file_compression_type>
The familiar 4 character PDB accession code will be extended to 8
characters and will include the prefix “pdb”. Thus PDB accession code
for entry 1abc would become pdb_00001abc.
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 zipped 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 will be stored in single
directory following a 2 character hash from the penultimate two
characters of the PDB code:
../pub/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:
../pub/pdb_versioned/data/entries/ab/pdb_00001abc/pdb_00001abc_xyz_v1-2.cif.gz
Different views of the repository will be provided for the most common
use cases as a convenience for repository users. For 2017 phase 1, views
by content type and format similar to the current repository will be
introduced. All latest major versions are included.
../pub/pdb_versioned/views/<content_type>/<file_format_type>/<two-letter-hash>/<pdb_accession_code>/<entry_data_File_names>
For example, the coordinate files in mmCIF format for entry 1ABC will be
made available at
../pub/pdb_versioned/views/coordinates/mmcif/ab/pdb_00001abc/pdb_00001abc_xyz_v1-2.cif.gz
../pub/pdb_versioned/views/coordinates/mmcif/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 contain only the latest version for every
entry.
<https://www.wwpdb.org/news/news?year=2017#top>
--
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
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