PDB Archive

The PDB archive is availale from pdb.protein.osaka-u.ac.jp which is a complete mirror of wwPDB FTP site. Files are available via FTP and rsync protocol.

Using FTP protocol

Connect to ftp://pdb.protein.osaka-u.ac.jp/ 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 pdb.protein.osaka-u.ac.jp::
 
ftp Top level of ftp tree approximately 86 GB ( /pub/pdb )
ftp_data Data directory within ftp archive approximately 86 GB ( /pub/pdb/data )
ftp_derived Derived data directory within ftp archive approximately 553 MB ( /pub/pdb/derived_data )
ftp_doc Doc directory within ftp archive approximately 251 MB ( /pub/pdb/doc )

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

rsync -a pdb.protein.osaka-u.ac.jp::ftp_data/structures/divided/pdb/ ./pdb

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

rsync -a pdb.protein.osaka-u.ac.jp::ftp_data/structures/divided/mmCIF/ ./mmCIF

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

rsync -a pdb.protein.osaka-u.ac.jp::ftp_data/structures/divided/XML/ ./XML

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 pdbjsnap.protein.osaka-u.ac.jp.

Using FTP protocol

Connect to ftp://pdbjsnap.protein.osaka-u.ac.jp/ 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 pdbjsnap.protein.osaka-u.ac.jp::

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

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

rsync -a pdbjsnap.protein.osaka-u.ac.jp::20050106 20050106_snapshot