The remediated PDB archive is availale from ftp://pdb.protein.osaka-u.ac.jp/v3/ which is a complete mirror of wwPDB FTP site. Files are available via FTP or rsync protocol. Yearly snapshots of PDB archives are available from PDBj snapshot site (a mirror server of PDB Archive Snapshot site). The final unremediated PDB snapshot is 20070731. 20070731 snapshot is also available at ftp://pdb.protein.osaka-u.ac.jp/pub/pdb/ for a meantime.

Using FTP protocol

Connect to ftp://pdb.protein.osaka-u.ac.jp/v3/ 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 55 GB
( /v3/pub/pdb )
ftp_data Data directory within ftp archive approximately 54.5 GB
( /v3/pub/pdb/data )
ftp_derived Derived data directory within ftp archive approximately 88 MB
( /v3/pub/pdb/derived_data )
ftp_doc Doc directory within ftp archive approximately 211 MB
( /v3/pub/pdb/doc )
ftp_software Software directory within ftp archive approximately 16 MB
( /v3/pub/pdb/software )

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

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