wwPDB: PDB Archive Downloads

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<li class='active'><a href='/ftp/pdb-ftp-sites' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDB Archive</a></li> <li ><a href='/ftp/pdb-versioned-ftp-site' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDB Versioned Archive</a></li> <li ><a href='/ftp/pdb-nextgen-archive-site' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDB NextGen Archive </a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <h1>PDB Archive Downloads</h1> <a href="#newSeqIn">New Sequence and InChI</a> <br/> <a href="#dataStCon">Data Structure and Content</a> <br/> <a href="#downloadPor">Download Protocols</a> <br/> <br/> <p>Please note that the FTP file download protocol in the PDB archive will be deprecated on November 1st 2024 (<a href="/news/news?year=2023#65562f0ad78e004e766a96c1">announcement</a>). </p> <p>The PDB archive and versioned archive are updated every Wednesday at 00:00 UTC.</p> <p> wwPDB: <a href="https://files.wwpdb.org" target="_blank">https://files.wwpdb.org</a>, rsync://rsync.wwpdb.org<br /> RCSB PDB (US): <a href="https://files.rcsb.org" target="_blank">https://files.rcsb.org</a>, rsync://rsync.rcsb.org (see the <a href="#downloadPor">download protocol below</a>)<br /> RCSB PDB (US/AWS): <a href="https://s3.rcsb.org" target="_blank">https://s3.rcsb.org</a><br /> PDBe (UK): <a href="ftp://ftp.ebi.ac.uk/pub/databases/pdb/" target="_blank">ftp.ebi.ac.uk/pub/databases/pdb/</a><br /> PDBj (Japan): <a href="ftp://ftp.pdbj.org" target="_blank">ftp://ftp.pdbj.org</a>, <a href="https://files.pdbj.org" target="_blank">https://files.pdbj.org</a>, rsync://rsync.pdbj.org </p> <p>The versioned FTP sites (<a href="https://www.wwpdb.org/news/news?year=2017#59cd3fa822e913222ac88fcd">See announcement</a>) are updated the same time when the main FTP sites are updated. </p> <p> wwPDB: <a href="https://files-versioned.wwpdb.org" target="_blank">https://files-versioned.wwpdb.org</a>, rsync://rsync-versioned.wwpdb.org<br /> RCSB PDB (US): <a href="https://files-versioned.rcsb.org" target="_blank">https://files-versioned.rcsb.org</a>, rsync://rsync-versioned.rcsb.org<br /> PDBe (UK): <a href="ftp://ftp.ebi.ac.uk/pub/databases/pdb_versioned/" target="_blank">ftp://ftp.ebi.ac.uk/pub/databases/pdb_versioned/</a><br /> PDBj (Japan): <a href="ftp://ftp-versioned.pdbj.org/" target="_blank">ftp://ftp-versioned.pdbj.org/</a>, <a href="https://files-versioned.pdbj.org" target="_blank">https://files-versioned.pdbj.org</a>, rsync://rsync-versioned.pdbj.org </p> <a name="newSeqIn" class="anchor"></a> <h2>New Sequence and InChI</h2> <p>Every Saturday by 3:00 UTC, for every new entry the wwPDB website provides: <ul> <li>Sequence(s) (amino acid or nucleotide) for each distinct polymer (<a href="/files/new_release_structure_sequence.tsv" target="_blank">new_release_structure_sequence.tsv</a>)</li> <li>InChI string(s) for each distinct ligand (<a href="/files/new_release_structure_nonpolymer.tsv" target="_blank">new_release_structure_nonpolymer.tsv</a>), where appropriate </li> <li>Crystallization pH value(s) (<a href="/files/new_release_crystallization_pH.tsv" target="_blank">new_release_crystallization_pH.tsv</a>)</li> </ul> </p> <a name="dataStCon" class="anchor"></a> <h2>Data Structure and Content</h2> <p>Primary data (atomic coordinates and experimental data) are stored using a hash directory. </p> <table class="table table-striped table-bordered text-left"> <tbody> <tr> <th>Data types</th> <th>File formats</th> <th>Location</th> </tr> <tr> <td>Atomic coordinates</td> <td>PDBx/mmCIF, XML, and PDB</td> <td><a href="https://files.wwpdb.org/pub/pdb/data/structures/" target="_blank">https://files.wwpdb.org/pub/pdb/data/structures/</a></td> </tr> <tr> <td>X-ray data: Structure Factors</td> <td>PDBx/mmCIF</td> <td><a href="https://files.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/" target="_blank">https://files.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/</a></td> </tr> <tr> <td>NMR data: Restraints and chemical shifts</td> <td>NEF (/nmr_data), NMR-STAR, and native refinement program formats</td> <td><a href="https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/" target="_blank">https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/</a><br/><a href="https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints_v2/" target="_blank">https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints_v2/</a><br/><a href="https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints/" target="_blank">https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints/</a><br/><a href="https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/" target="_blank">https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/</a></td> </tr> <tr> <td>Small molecules references: CCD and BIRD</td> <td>PDBx/mmCIF</td> <td><a href="https://files.wwpdb.org/pub/pdb/refdata/chem_comp/" target="_blank">https://files.wwpdb.org/pub/pdb/refdata/chem_comp/</a><br/><a href="https://files.wwpdb.org/pub/pdb/refdata/bird" target="_blank">https://files.wwpdb.org/pub/pdb/refdata/bird</a></td> </tr> <tr> <td>Assemblies</td> <td>PDBx/mmCIF, PDB</td> <td><a href="https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/" target="_blank">https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/</a><br/><a href="https://files.wwpdb.org/pub/pdb/data/biounit/PDB/" target="_blank">https://files.wwpdb.org/pub/pdb/data/biounit/PDB/</a></td> </tr> <tr> <td>Archive holdings</td> <td>JSON</td> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/" target="_blank">https://files.wwpdb.org/pub/pdb/holdings/</a></td> </tr> <tbody> </table> <h3>List of archive holdings</h3> <p>These inventory data files at /pub/pdb/holdings/ offer a quick overview of data in the archive.</p> <table class="table table-striped table-bordered text-left"> <tbody> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/current_file_holdings.json.gz" target="_blank">current_file_holdings.json.gz</a></td> <td>a list of released PDB entries and the file types present for each in the PDB Core Archive (e.g. coordinate data, experimental data, validation report).</td> </tr> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/refdata_id_list.json.gz" target="_blank">refdata_id_list.json.gz</a></td> <td>a list of released chemical reference entries, their content types (e.g., Chemical Component, BIRD), and the most recent modification date of the reference file.</td> </tr> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/released_structures_last_modified_dates.json.gz" target="_blank">released_structures_last_modified_dates.json.gz</a></td> <td>a list of released PDB entries with the most recent modification date of the PDBx/mmCIF file.</td> </tr> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/released_experimental_data_last_modified_dates.json.gz" target="_blank">released_experimental_data_last_modified_dates.json.gz </a></td> <td>a list of released experimental data files with the most recent modification date.</td> </tr> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/obsolete_structures_last_modified_dates.json.gz" target="_blank">obsolete_structures_last_modified_dates.json.gz</a></td> <td>a list of obsoleted PDB entries with the most recent modification date of the PDBx/mmCIF file.</td> </tr> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/obsolete_experimental_data_last_modified_dates.json.gz" target="_blank">obsolete_experimental_data_last_modified_dates.json.gz</a></td> <td>a list of obsoleted experimental data files with the most recent modification date.</td> </tr> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/all_removed_entries.json.gz" target="_blank">all_removed_entries.json.gz</a></td> <td>a list of obsoleted PDB entries including information for entry authors, entry title, release date, obsolete date, and superseding PDB ID, if any.</td> </tr> <tr> <td><a href="https://files.wwpdb.org/pub/pdb/holdings/unreleased_entries.json.gz" target="_blank">unreleased_entries.json.gz</a></td> <td>a list of on-hold PDB entries, their entry status, deposition date, and pre-release sequence information, where available.</td> </tr> <tbody> </table> <a name="downloadPor" class="anchor"></a> <h2>Download Protocols</h2> <p> Every Wednesday from 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB repository sites. The PDB archive is quite large, requiring over 1TB of storage, and continues to grow with each weekly update. </p> <p>All files mentioned above are available via 3 different protocols: ftp, https and rsync. For individual file downloads we recommend https. The ftp protocol will be gradually phased out. For bulk file downloads we recommend rsync, see more instructions about rsync below.</p> <p> Download instructions for: <a class="b" href="#rcsbpdb">RCSB PDB (USA)</a> | <a class="b" href="#msdebi">PDBe (UK) </a> | <a class="b" href="#pdbj">PDBj (Japan)</a> </p>  <h3 class="underline" id="rcsbpdb">RCSB PDB:</h3> <p class="b" style="text-transform:uppercase;"> Using rsync protocol: </p> <pre class="pre"> rsync --port=33444 rsync.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 ) </pre> <p> <b class="b">Download coordinate files in PDB Exchange Format (mmCIF): </b> </p> <pre class="pre"> rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ ./mmCIF </pre> <p> <b class="b"> Download coordinate files in PDBML Format (xml):</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp_data/structures/divided/XML/ ./XML </pre> <p> <b class="b">Download coordinate files in PDB Format:</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp_data/structures/divided/pdb/ ./pdb </pre> <p> <b class="b">Download EMDB map metadata header files (xml):</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete --port=33444 --include "emd-*.xml" \ "rsync.rcsb.org::emdb/structures/EMD-*/header/" ./header </pre> <p> <b class="b">Download directories/files for EMDB entry EMD-5001:</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::emdb/structures/EMD-5001/ ./EMD-5001 </pre> <p> <b class="b">Download the validation report files: </b> </p> <pre class="pre"> rsync -rlpt -v -z --delete --port=33444 \ rsync.rcsb.org::ftp/validation_reports/ ./validation_reports </pre> <p> <b class="b">Download coordinate files in PDB Exchange Format (mmCIF): </b> </p> <pre class="pre"> <a href="https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF" class="pre b" target="_blank">https://files.rcsb.org/pub/pdb/data/structures/divided/mmCIF</a> </pre> <p> <b class="b">Download coordinate files in PDBML format:</b> </p> <pre class="pre"> <a href="https://files.rcsb.org/pub/pdb/data/structures/divided/XML" class="pre b" target="_blank">https://files.rcsb.org/pub/pdb/data/structures/divided/XML</a> </pre> <p> <b class="b">Download coordinate files in PDB format:</b> </p> <pre class="pre"> <a href="https://files.rcsb.org/pub/pdb/data/structures/divided/pdb" class="pre b" target="_blank">https://files.rcsb.org/pub/pdb/data/structures/divided/pdb</a> </pre> <p> <b class="b">Download EMDB data files:</b> </p> <pre class="pre"> <a href="https://files.rcsb.org/pub/emdb/structures" class="pre b" target="_blank">https://files.rcsb.org/pub/emdb/structures</a> </pre> <p> <b class="b">Download the validation report files:</b> </p> <pre class="pre"> <a href="https://files.rcsb.org/pub/pdb/validation_reports" class="pre b" target="_blank">https://files.rcsb.org/pub/pdb/validation_reports</a> </pre> <p> <b class="b">Need further help with the US site:</b> Please contact <a href="mailto:info@rcsb.org">info@rcsb.org</a> if you have any problems connecting to ftp.rcsb.org. </p>   <h3 class="underline" id="msdebi">PDBe:</h3> <p> <b class="b" style="text-transform:uppercase;">Using rsync protocol:</b> </p> <pre class="pre"> rsync rsync.ebi.ac.uk:: pub ftp.ebi.ac.uk /pub area </pre> <p> <b class="b">Download coordinate files in PDB Exchange Format (mmCIF):</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete \ rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ \ ./mmCIF </pre> <p> <b class="b">Download coordinate files in PDBML Format (xml):</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete \ rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/XML/ \ ./XML </pre> <p> <b class="b">Download coordinate files in PDB Format:</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete \ rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/pdb/ \ ./pdb </pre> <p> <b class="b">Download EMDB map metadata header files (xml):</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete --include "emd-*.xml" \ "rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-*/header/" ./header </pre> <p> <b class="b">Download directories/files for EMDB entry EMD-1003:</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete \ rsync.ebi.ac.uk::pub/databases/emdb/structures/EMD-1003/ ./EMD-1003 </pre> <p> <b class="b">Download the validation report files:</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete \ rsync.ebi.ac.uk::pub/databases/pdb/validation_reports/ \ ./validation_reports </pre> <p class="b" style="text-transform:uppercase;"> Using ftp protocol: </p> <pre class="pre"> ftp <a href="https://ftp.ebi.ac.uk" class="pre b" target="_blank">ftp.ebi.ac.uk</a> </pre> <p> will connect to an anonymous ftp server containing the remediated wwPDB repository. </p> <p> <b class="b">Download coordinate files in PDB Exchange Format (mmCIF): </b> </p> <pre class="pre"> <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF" class="pre b" target="_blank"> https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF </a> </pre> <p> <b class="b">Download coordinate files in PDBML format:</b> </p> <pre class="pre"> <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/XML" class="pre b" target="_blank"> https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/XML </a> </pre> <p> <b class="b">Download coordinate files in PDB format:</b> </p> <pre class="pre"> <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/pdb" class="pre b" target="_blank"> https://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/pdb </a> </pre> <p> <b class="b">Download the full PDB ftp tree: </b> </p> <pre class="pre"> <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/" class="pre b" target="_blank">https://ftp.ebi.ac.uk/pub/databases/pdb/</a> </pre> <p> <b class="b">Download EMDB data files:</b> </p> <pre class="pre"> <a href="https://ftp.ebi.ac.uk/pub/databases/emdb/structures" target="_blank">https://ftp.ebi.ac.uk/pub/databases/emdb/structures</a> </pre> <p> <b class="b">Download the validation report files: </b> </p> <pre class="pre"> <a href="https://files.ebi.ac.uk/pub/databases/pdb/validation_reports" class="pre b" target="_blank"> https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports </a> </pre> <p> <b>Need further help with the PDBe site:</b> Please contact PDBe (<a href="http://www.ebi.ac.uk/pdbe/about/contact" target="_blank">http://www.ebi.ac.uk/pdbe/about/contact</a> or e-mail <a href="mailto:pdbehelp@ebi.ac.uk">pdbehelp@ebi.ac.uk</a>) if you have any problems connecting to ftp.ebi.ac.uk. </p>   <h3 id="pdbj" class="underline">PDBj:</h3> <p> <b class="b" style="text-transform: uppercase;">Using rsync protocol:</b> </p> <pre class="command"> rsync ftp.pdbj.org:: ftp Top level of PDB ftp tree approximately ( /pub/pdb ) ftp_data Data directory within PDB ftp archive Approximately ( /pub/pdb/data ) ftp_derived Derived data directory within PDB ftp archive Approximately ( /pub/pdb/derived_data ) ftp_doc Doc directory within PDB ftp archive Approximately ( /pub/pdb/doc ) emdb Top level of EMDB ftp tree Approximately ( /pub/emdb ) rsync Top level of PDBj FTP tree aproximately ( / ) </pre> <p> <b class="b">Download coordinate files in PDB Exchange Format (mmCIF): </b> </p> <pre class="pre"> rsync -rlpt -v -z --delete \ ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ ./mmCIF </pre> <p> <b class="b"> Download coordinate files in PDBML Format (xml):</b> </p> <pre class="pre"> rsync -rlpt -v -z --delete \ ftp.pdbj.org::ftp_data/structures/divided/XML/ ./XML </pre> <p> <b class="b">Download coordinate files in PDB Format:</b> </p> <pre 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