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PDB Archive

The PDB FTP sites are updated every Wednesday at 00:00 UTC / 09:00 JST.

The latest PDB raw data is available under the PDB Archive site.

  • The available protocols are http, ftp, and rsync.
  • There are two types of archive site: the main archive (ftp.pdbj.org) includes the latest PDB data only and the versioned archive (ftp-versioned.pdbj.org) includes each major version.
  • The PDB archive provided from PDBj includes completely equal data to the archive from wwPDB.
  • Our archive provides the secondary data such as PDBMLadd and mmjson created by PDBj as well as the wwPDB common data.
Archives Protocols
http ftp rsync
Main Archive http://ftp.pdbj.org/ ftp://ftp.pdbj.org/ rsync -az ftp.pdbj.org::
Versioned Archive http://ftp-versioned.pdbj.org/ ftp://ftp-versioned.pdbj.org/ rsync -az ftp-versioned.pdbj.org::

See also "About contents in PDBj FTP site" page.

Using FTP protocol

Connect to PDBj FTP site using your prefered FTP client.

Using rsync protocol

It is useful for whole/partial mirroring of PDB archive. Several entry points are provided which can be viewed using the following command:

 $ rsync ftp.pdbj.org::
Welcome to PDBj FTP site.

ftp         Top level of pdb data ftp tree aproximately 528 GB ( /pub/pdb )
ftp_data    Data directory within ftp archive aproximately 356 GB ( /pub/pdb/data )
ftp_derived Derived data directory within ftp archive aproximately 280 MB ( /pub/pdb/derived_data )
ftp_doc     Doc directory within ftp archive aproximately 372 MB ( /pub/pdb/doc )
emdb        Top level of emdb data ftp tree aproximately 1.3 TB ( /pub/emdb )
rsync       Top level of PDBj FTP tree aproximately 4.2 TB ( / )

To download the entry files in PDB format the following rsync command may be used:

rsync -avz --delete ftp.pdbj.org::ftp_data/structures/divided/pdb/ ./pdb

To download the entry files in PDB exchange format (mmCIF) the following rsync command may be used:

rsync -avz --delete ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ ./mmCIF

To download the entry files in PDBML format the following rsync command may be used:

rsync -avz --delete ftp.pdbj.org::ftp_data/structures/divided/XML/ ./XML

To download the entry files in EMDB format the following rsync command may be used:

rsync -avz --delete ftp.pdbj.org::emdb/ ./emdb

[Snapshot Archive]

wwPDB provides snapshot archive which have the snapshots of the FTP archive just before the first release in every year or the remediaion at wwPDB Archive Snapshots site. The complete mirror is available from snapshots.pdbj.org.

Using FTP protocol

Connect to ftp://snapshots.pdbj.org/ using your prefered FTP client.

Using rsync protocol

It is useful for whole/partial mirroring of shapshot archive. Several entry points are provided which can be viewed using the following command:

 $ rsync snapshots.pdbj.org::

all             Entire Snapshots archive
20050106        January 6, 2005 snapshot
20060103        January 3, 2006 snapshot
20070102        January 2, 2007 snapshot
20070731        July 31, 2007 snapshot
20080107        January 7, 2008 snapshot
20090105        January 5, 2009 snapshot
20090316        March 16, 2009 snapshot
20100104        January 4, 2010 snapshot
20110103        January 3, 2011 snapshot
20110707        July 7, 2011 snapshot
20120102        January 2, 2012 snapshot
20130101        January 1, 2013 snapshot
20140102        January 2, 2014 snapshot
20141203        December 3, 2014 snapshot
20150102        January 2, 2015 snapshot
20160101        January 1, 2016 snapshot
20160302        March 2, 2016 snapshot (Validation Reports Only)
20170101        January 1, 2017 snapshot
20170308        March 8, 2017 snapshot (Validation Reports Only)
20170710        July 10, 2017 snapshot
20180101        January 1, 2018 snapshot
20180321        March 21, 2018 snapshot (Validation Reports Only)
20190101        January 1, 2019 snapshot

To download 2005-01-06 shapshot and put them to 20050106_snapshot directory may be used:

rsync -a snapshots.pdbj.org::20050106 20050106_snapshot
Created: 2012-03-30 (last edited: 4 months ago)2019-07-03