wwPDB Welcome to the Worldwide Protein Data Bank
Access the PDB FTP:
RCSB PDB | PDBe | PDBj
Archive Download
Chemical Component Dictionary
Biologically Interesting Molecule Reference Dictionary (BIRD)
New Deposition and Annotation System
Tutorial
System Information
FAQ
Validation Reports
Reports
Server Information
Deposit Data to the PDB:
RCSB PDB | PDBe
PDBj | BMRB
Search for Structures:
RCSB PDB | PDBe
PDBj | BMRB
PDB Archive Snapshots:
RCSB PDB | PDBj
Instructions to Journals
Documentation: Format, Annotation and Policies, Remediation
Workshops and Task Forces
X-ray Validation
NMR Validation
EM Validation
SAS Task Force
PDBx/mmCIF Working Group
Past Symposia
Int'l Year of Crystallography
wwPDBAC
EMDB

Data Download Details

The PDB FTP archive is quite large. As of May 14, 2014, the entire server contains more than 1,200,000 files requiring over 373 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.

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Please note: ftp://ftp.rcsb.org is no longer updated.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 PDB ftp tree approximately 130 GB ( /pub/pdb )
ftp_data       	Data directory within PDB ftp archive Approximately 129 GB ( /pub/pdb/data )
ftp_derived    	Derived data directory within PDB ftp archive Approximately 120 MB ( /pub/pdb/derived_data )
ftp_doc        	Doc directory within PDB ftp archive Approximately 319 MB ( /pub/pdb/doc )
emdb		Top level of EMDB ftp tree approximately 47 GB ( /pub/emdb )

Download coordinate files in PDB Exchange Format (mmCIF):

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

Download coordinate files in PDBML Format (xml):

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

Download coordinate files in PDB Format:

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

Download directories/files for EMDB entry EMD-5001:

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

Download the validation report files:

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

Using ftp protocol:

ftp ftp.wwpdb.org

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

Download coordinate files in PDB Exchange Format (mmCIF):

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

Download coordinate files in PDBML format:

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

Download coordinate files in PDB format:

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

Download EMDB data files:

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

Download the validation report files:

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

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

Download coordinate files in PDB Exchange Format (mmCIF):

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

Download coordinate files in PDBML Format (xml):

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

Download coordinate files in PDB Format:

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

Download coordinate files in PDBML format:

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

Download coordinate files in PDB format:

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

Download the full PDB ftp tree:

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

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/rcsb/pdb-remediated/validation_reports

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 ftp://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


© wwPDB