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Data Download DetailsThe wwPDB ftp site is quite large. As of March 7, 2012, it contains more than 610,000 files requiring over 186 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)
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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 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 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/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 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 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.pdbj.org:: 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 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 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 |