Data Download Details

The wwPDB ftp site is quite large. As of January 1, 2008, it contains more than 300,000 files and requires over 70 GBbytes of storage, and will continue to grow with each weekly update. Fresh downloads will require substantial amount of time.

A number of download locations and options are provided to make access as efficient as possible.

Access is available from: the RCSB PDB (USA) | PDBe (UK) | PDBj (Japan)

RCSB PDB:

Using rsync protocol: Anonymous rsync access is also provided to the remediated site in the US. Several entry points are provided which can be viewed using the following command:

rsync --port=33444 ftp.wwpdb.org::
 
ftp Top level of ftp tree approximately 72 GB
(/pub/pdb )
ftp_data Data directory within ftp archive approximately 71 GB
(/pub/pdb/data )
ftp_derived Derived data directory within ftp archive approximately 296 MB
(/pub/pdb/derived_data )
ftp_doc Doc directory within ftp archive approximately 233 MB
(/pub/pdb/doc )

Using ftp protocol:

ftp ftp.wwpdb.org

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

rsync -a --port=33444 \

ftp.wwpdb.org::ftp_data/structures/divided/mmCIF/ ./mmCIF

Downloading coordinate files in PDBML Format (xml): To download the entry files in PDBML format the following rsync command may be used:

rsync -a --port=33444 \

ftp.wwpdb.org::ftp_data/structures/divided/XML/ ./XML

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

rsync -a --port=33444 \

ftp.wwpdb.org::ftp_data/structures/divided/pdb/ ./pdb

Need further help with the US site: Please contact Wolfgang Bluhm (wbluhm@ucsd.edu) if you have any problems connecting to ftp.wwpdb.org.

PDBe:

Using the rsync protocol:

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

rsync -a \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/data/structures/divided/mmCIF/ \
./mmCIF

Downloading coordinate files in PDBML Format (xml): To download the entry files in PDBML format the following rsync command may be used:

rsync -a \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/data/structures/divided/XML/ \
./XML

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

rsync -a \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb/ \
./pdb

Using ftp protocol:

ftp ftp.ebi.ac.uk 

Downloading coordinate files in PDB Exchange Format (mmCIF): To download the entry files in PDB exchange format use the following entry point:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/mmCIF

Downloading coordinate files in PDBML format: To download the entry files in PDBML format use the following entry point:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/XML

Downloading coordinate files in PDB format: To download the entry files in PDB format use the following entry point:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb

Downloading the full ftp tree: To download the full remediated ftp tree use the following entry point:

ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/

Need further help with the EBI site: Please contact Gaurav Sahni (gaurav@ebi.ac.uk) if you have any problems connecting to ftp.ebi.ac.uk.

PDBj:

Using rsync protocol: rsync is useful for whole/partial mirroring of the 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 
( /v3/pub/pdb )
ftp_data Data directory within ftp archive approximately 
( /v3/pub/pdb/data )
ftp_derived Derived data directory within ftp archive approximately 
( /v3/pub/pdb/derived_data )
ftp_doc Doc directory within ftp archive approximately 
( /v3/pub/pdb/doc )

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/strucrures/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/strucrures/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/strucrures/divided/pdb/ ./pdb

Using ftp protocol:

ftp pdb.protein.osaka-u.ac.jp/

Downloading coordinate files in PDB Exchange Format (mmCIF): To download the entry files in PDB exchange format, use the following entry point:

ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/data/structures/divided/mmCIF/

Downloading coordinate files in PDBML format (all): To download the entry files in PDBML format with the full-tag representation, use the following entry point:

ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/data/structures/divided/XML/

Downloading coordinate files in PDBML format (no-atom): To download the entry files in PDBML format without atom site information, use the following entry point:

ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/data/structures/divided/XML-noatom/

Downloading coordinate files in PDBML format (ext-atom): To download the entry files in PDBML format only for the atom site information, use the following entry point:

ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/data/structures/divided/XML-extatom/

Downloading coordinate files in PDB format: To download the entry files in PDB format use the following entry point:

ftp://pdb.protein.osaka-u.ac.jp/v3/pub/pdb/data/structures/divided/pdb//

Need further help with the PDBj site: Please contact PDBj from http://www.pdbj.org/second/pdbj_contact.html if you have any problems connecting to pdb.protein.osaka-u.ac.jp