PDB FTP Sites

The PDB FTP sites are updated every Wednesday at 00:00 UTC.

wwPDB: ftp.wwpdb.org
RCSB PDB (USA): ftp.rcsb.org
PDBe (UK): ftp.ebi.ac.uk/pub/databases/pdb/
PDBj (Japan): ftp.pdbj.org

Download Weekly Release of New Sequence and InChI

Every Saturday by 3:00 UTC, for every new entry, the wwPDB website provides: sequence(s) (amino acid or nucleotide) for each distinct polymer (new_release_structure_sequence.tsv) and, where appropriate, the InChI string(s) for each distinct ligand (new_release_structure_nonpolymer.tsv) and the crystallization pH value(s) (new_release_crystallization_pH.tsv).

Download Archive - Data Download Instructions

Every Wednesday from 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites. The PDB FTP archive is quite large. As of January 1, 2017, the entire server contains more than 1,600,000 files requiring over 757 GBbytes of storage. It continues to grow with each weekly update.

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

Download instructions for: the RCSB PDB (USA) | PDBe (UK) | PDBj (Japan)

RCSB PDB:

Using rsync protocol:

rsync --port=33444 ftp.rcsb.org::
ftp             Top level of PDB ftp tree ( /pub/pdb )
ftp_data        Data directory within PDB ftp archive ( /pub/pdb/data )
ftp_derived     Derived data directory within PDB ftp archive ( /pub/pdb/derived_data )
ftp_doc         Doc directory within PDB ftp archive ( /pub/pdb/doc )
emdb            Top level of EMDB ftp tree ( /pub/emdb )

Download coordinate files in PDB Exchange Format (mmCIF):

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

Download coordinate files in PDBML Format (xml):

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

Download coordinate files in PDB Format:

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

Download EMDB map metadata header files (xml):

rsync -rlpt -v -z --delete --port=33444 --include "emd-*.xml" \
"rsync.rcsb.org::emdb/structures/EMD-*/header/" ./header

Download directories/files for EMDB entry EMD-5001:

rsync -rlpt -v -z --delete --port=33444 \
rsync.rcsb.org::emdb/structures/EMD-5001/ ./EMD-5001

Download the validation report files:

rsync -rlpt -v -z --delete --port=33444 \
rsync.rcsb.org::ftp/validation_reports/ ./validation_reports

Using ftp protocol:

ftp ftp.rcsb.org

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

Download coordinate files in PDB Exchange Format (mmCIF):

ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/mmCIF

Download coordinate files in PDBML format:

ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/XML

Download coordinate files in PDB format:

ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/pdb

Download EMDB data files:

ftp://ftp.rcsb.org/pub/emdb/structures

Download the validation report files:

ftp://ftp.rcsb.org/pub/pdb/validation_reports

Need further help with the US site: Please contact info@rcsb.org if you have any problems connecting to ftp.rcsb.org.

PDBe:

Using rsync protocol:

rsync rsync.ebi.ac.uk::    pub                ftp.ebi.ac.uk /pub area

Download coordinate files in PDB Exchange Format (mmCIF):

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

Download coordinate files in PDBML Format (xml):

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

Download coordinate files in PDB Format:

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

Download EMDB map metadata header files (xml):

rsync -rlpt -v -z --delete --include "emd-*.xml" \
"rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-*/header/" ./header

Download directories/files for EMDB entry EMD-1003:

rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-1003/ ./EMD-1003

Download the validation report files:

rsync -rlpt -v -z --delete \
rsync.ebi.ac.uk::pub/databases/pdb/validation_reports/ \
./validation_reports

Using ftp protocol:

ftp ftp.ebi.ac.uk

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

Download coordinate files in PDB Exchange Format (mmCIF):


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

Download coordinate files in PDBML format:


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

Download coordinate files in PDB format:


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

Download the full PDB ftp tree:

ftp://ftp.ebi.ac.uk/pub/databases/pdb/

Download EMDB data files:

ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures

Download the validation report files:


ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports

Need further help with the PDBe site: Please contact PDBe (http://www.ebi.ac.uk/pdbe/about/contact or e-mail pdbehelp@ebi.ac.uk) if you have any problems connecting to ftp.ebi.ac.uk.

PDBj:

Using rsync protocol:

rsync ftp.pdbj.org::

ftp             Top level of PDB ftp tree approximately 145 GB ( /pub/pdb )
ftp_data        Data directory within PDB ftp archive Approximately 144 GB ( /pub/pdb/data )
ftp_derived     Derived data directory within PDB ftp archive Approximately 130 MB ( /pub/pdb/derived_data )
ftp_doc         Doc directory within PDB ftp archive Approximately 331 MB ( /pub/pdb/doc )
emdb            Top level of EMDB ftp tree Approximately 49 GB ( /pub/emdb )
rsync           Top level of PDBj FTP tree aproximately 423 GB ( / )

Download coordinate files in PDB Exchange Format (mmCIF):

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ ./mmCIF

Download coordinate files in PDBML Format (xml):

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/XML/ ./XML

Download coordinate files in PDB Format:

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp_data/structures/divided/pdb/ ./pdb

Download EMDB map metadata header files (xml):

rsync -rlpt -v -z --delete --include "emd-*.xml" \
"ftp.pdbj.org::emdb/structures/EMD-*/header/" ./header

Download directories/files for EMDB entry EMD-5001:

rsync -rlpt -v -z --delete \
ftp.pdbj.org::emdb/structures/EMD-5001/ ./EMD-5001

Download the validation report files:

rsync -rlpt -v -z --delete \
ftp.pdbj.org::ftp/validation_reports/ ./validation_reports

Using ftp protocol:

ftp ftp.pdbj.org

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

Download coordinate files in PDB Exchange Format (mmCIF):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/mmCIF/

Download coordinate files in PDBML format (all):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML/

Download coordinate files in PDBML format (no-atom site information):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-noatom/

Download coordinate files in PDBML format (atom site information only):

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/XML-extatom/

Download coordinate files in PDB format:

ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/pdb/

Download EMDB data files:

ftp://ftp.pdbj.org/pub/emdb/structures

Download the validation report files:

ftp://ftp.pdbj.org/pub/pdb/validation_reports/

Need further help with the PDBj site: Please contact PDBj http://www.pdbj.org/pdbj_contact.html if you have any problems connecting to ftp.pdbj.org