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
20200101 January 1, 2020 snapshot
20200610 June 10, 2020 snapshot (Validation Reports Only)
20200722 July 22, 2020 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
