<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">wwPDB news: <a href="http://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8" class="">http://www.wwpdb.org/news/news?year=2017#5910c8d8d3b1d333029d4ea8</a></div><div class="">
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<h2 class="">Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive</h2><p class="">The
wwPDB is planning to introduce in 2017 a new procedure for the
management by the Depositor of Record (where the Depositor of Record is
defined as the Principal Investigator for the entry) of substantial
revisions to previously released PDB archival entries.</p><p class="">At present,
revised atomic coordinates for an existing released PDB entry are
assigned a new accession code, and the prior entry is obsoleted. This
long-standing wwPDB policy had the unintended consequence of breaking
connections with publications and usage of the prior set of atomic
coordinates, resulting in a non-trivial barrier to submission of atomic
coordinate revisions by our Depositors of Record.</p><p class="">The wwPDB is
introducing a file versioning system that allows Depositors of Record to
update their own previously released entries. Please note, in the first
phase, file versioning will be applied to the atomic coordinates
refined versus unchanged experimental data.</p><p class="">Version numbers of
each PDB archive entry will be designated using a #-# identifier. The
first digit specifies the major version, and the second designates the
minor version. The Structure of Record (i.e., the initial set of
released atomic coordinates) is designated as Version 1-0. Thereafter,
the major version digit is incremented with each substantial revision of
a given entry (e.g., Version 2-0, when the atomic coordinates are
replaced for the first time by the Depositor of Record). “Major version
changes” are defined as updates to the atomic coordinates, polymer
sequence(s), and/or chemical identify of a ligand. All other changes are
defined as “minor changes”. When a major change is made, the minor
version number is reset to 0 (e.g., 1-0 to 1-1 to 2-0). For the
avoidance of doubt, the wwPDB will retain all major versions with the
latest minor versions of an entry within the PDB archive.</p><p class="">Current
wwPDB policies governing the deposition of independently refined
structures based on the data generated by a research group or laboratory
separate from that of the Depositor of Record remain unchanged.
Versioning of atomic coordinates will be strictly limited to
substitutions made by the Depositor of Record.</p><p class="">Upon introduction
of the file versioning system, the wwPDB will revise each PDB accession
code by extending its length and prepending “PDB” (e.g., "1abc" will
become "pdb_00001abc"). This process will enable text mining detection
of PDB entries in the published literature and allow for more
informative and transparent delivery of revised data files. For example,
the atomic coordinates for the second major version of PDB entry 1abc
would have the following form under the new file-naming schema:</p><p class="">pdb_00001abc_xyz_v2-0.cif.gz</p><p class="">The
wwPDB is mindful of the importance of continuity in providing services
and supporting User activities. For as long as practicable, the wwPDB
will continue assigning PDB codes that can be truncated losslessly to
the current four-character style. In the same spirit, initial
implementation of entry file versioning will appear in a new, parallel
branch of the PDB archive FTP tree. More details on the new FTP tree
organization and accessibility of version information will be
forthcoming. Data files in the current archive location <a href="ftp://ftp.wwpdb.org/pub/pdb/data/structures/" class="">ftp://ftp.wwpdb.org/pub/pdb/data/structures/</a> will continue to use the familiar naming style and will contain the latest version in the corresponding versioned archive.</p></body></html>