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Data Download Details

The wwPDB ftp site is quite large. As of September 21, 2008, it contains more than 443,000 files and requires over 94 GBbytes of storage. It 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)

Please note: ftp://ftp.rcsb.org is no longer updated. Please access the PDB archive using one of the FTP sites listed in the left menu.

RCSB PDB:

Using rsync protocol:

rsync --port=33444 ftp.wwpdb.org::

ftp            	Top level of ftp tree approximately 66 GB ( /pub/pdb )
ftp_data       	Data directory within ftp archive Aproximately 65.7 GB ( /pub/pdb/data )
ftp_derived    	Derived data directory within ftp archive Aproximately 134 MB ( /pub/pdb/derived_data )
ftp_doc        	Doc directory within ftp archive Aproximately 234 MB ( /pub/pdb/doc )

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 -rlpt -v -z --delete --port=33444 \
rsync.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 -rlpt -v -z --delete --port=33444 \
rsync.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 -rlpt -v -z --delete --port=33444 \
rsync.wwpdb.org::ftp_data/structures/divided/pdb/ ./pdb

Using ftp protocol:

ftp ftp.wwpdb.org

will connect to an anonymous ftp server containing the remediated wwPDB repository.

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

ftp://ftp.wwpdb.org/pub/pdb/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.wwpdb.org/pub/pdb/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.wwpdb.org/pub/pdb/data/structures/divided/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 rsync protocol:

rsync rsync.ebi.ac.uk::

pub            	ftp.ebi.ac.uk /pub area

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 -rlpt -v -z --delete \
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 -rlpt -v -z --delete \
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 -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/rcsb/pdb-remediated/data/structures/divided/pdb/ \
./pdb

Using ftp protocol:

ftp ftp.ebi.ac.uk

will connect to an anonymous ftp server containing the remediated wwPDB repository.

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 pdb.protein.osaka-u.ac.jp::

ftp            	Top level of ftp tree aproximately 86 GB ( /pub/pdb )
ftp_data       	Data directory within ftp archive Aproximately 86 GB ( /pub/pdb/data )
ftp_derived    	Derived data directory within ftp archive Aproximately 553 MB ( /pub/pdb/derived_data )
ftp_doc        	Doc directory within ftp archive Aproximately 251 MB ( /pub/pdb/doc )

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 -rlpt -v -z --delete \
pdb.protein.osaka-u.ac.jp::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 -rlpt -v -z --delete \
pdb.protein.osaka-u.ac.jp::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 -rlpt -v -z --delete \
pdb.protein.osaka-u.ac.jp::ftp_data/structures/divided/pdb/ ./pdb

Using ftp protocol:

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

will connect to an anonymous ftp server at PDBj containing the remediated wwPDB repository.

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/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/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/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/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/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