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Search</a><a title="PDBj Omni Search Help" href="/help/omni-search">Search help</a></div></div></header><div><main id=""><div class="sNP" typeof="Article"><h1 property="name headline">How to download from the PDB/snapshot archive</h1><div><div class="OGhover opacityTransition2 _langList_" style="margin-left: 3em;"><span>This page is also available in: </span><a title="日本語" href="/info/archive?lang=ja" style="margin-right: 0.75em;">日本語</a><hr class="leftHR"></div><div property="articleBody" class="BLOG_BOX"> <style type="text/css"> .table { border: 1px solid gray; border-collapse: collapse; } .table th, .table td { border: 1px solid gray; padding: 0.5ex 0.5em; } .table th { background-color: #eee; } </style> <h2>PDB Archive</h2> <p> The PDB data sites are updated every Wednesday at 00:00 UTC / 09:00 JST. <br> ( The PDB NextGen Repositories are updated every month on the 1st Wednesday at 00:00 UTC / 09:00 JST.) </p> <p> The latest PDB raw data is available from the <b>PDB Archive</b> site. </p> <ul> <li>The available protocols are https, ftp, and rsync.</li> <li>There are two types of our archive site: the data archive (<a class="external" href="https://data.pdbjlc1.pdbj.org/" rel="nofollow noopener" target="_blank">data.pdbjlc1.pdbj.org</a>) that includes the latest PDBj data and the wwPDB archives (split into <a class="external" href="https://files.pdbj.org/" rel="nofollow noopener" target="_blank">files.pdbj.org</a> , <a class="external" href="https://files-versioned.pdbj.org/" rel="nofollow noopener" target="_blank">files-versioned.pdbj.org</a> and <a class="external" href="https://files-nextgen.pdbj.org/" rel="nofollow noopener" target="_blank">files-nextgen.pdbj.org</a>).</li> <li>The PDB archive provided by PDBj is a superset of the wwPDB data, including the original wwPDB data; <a class="external" href=" https://files.wwpdb.org" target="_blank" rel="nofollow noopener">core</a> , <a class="external" href="https://files-versioned.wwpdb.org" target="_blank" rel="nofollow noopener">versioned</a> , <a class="external" href="https://files-nextgen.wwpdb.org/" target="_blank" rel="nofollow noopener">nextgen</a>, and our own generated data and archives.</li> </ul> <table class="table"> <tbody><tr> <th rowspan="2">Archives</th> <th colspan="3">Protocols</th> </tr> <tr> <th>https</th> <th>ftp</th> <th>rsync</th> </tr> <tr> <td>wwPDB core Archives@PDBj</td> <td><a href="https://files.pdbj.org/" rel="nofollow noopener" target="_blank">https://files.pdbj.org/</a></td> <td>ftp://ftp.pdbj.org/</td> <td>rsync -az rsync.pdbj.org::</td> </tr> <tr> <td>wwPDB Versioned Archive@PDBj</td> <td><a href="https://files-versioned.pdbj.org/" rel="nofollow noopener" target="_blank">https://files-versioned.pdbj.org/</a></td> <td>ftp://ftp-versioned.pdbj.org/</td> <td>rsync -az rsync-versioned.pdbj.org::</td> </tr> <tr> <td>wwPDB next generation Archive@PDBj</td> <td><a href="https://files-nextgen.pdbj.org/" rel="nofollow noopener" target="_blank">https://files-nextgen.pdbj.org/</a></td> <td>ftp://ftp-nextgen.pdbj.org/</td> <td>rsync -az rsync-nextgen.pdbj.org::</td> </tr> <tr> <td>PDBj data Archive<br>(including wwPDB Archives)</td> <td><a href="https://data.pdbjlc1.pdbj.org/" rel="nofollow noopener" target="_blank">https://data.pdbjlc1.pdbj.org/</a></td> <td>ftp://data.pdbjlc1.pdbj.org/</td> <td>rsync -az data.pdbjlc1.pdbj.org::</td> </tr> </tbody></table> <p id="introduction2"> See also "<a href="/help/data_download">About the contents of the PDBj data site</a>" page. </p> <h3>Using the FTP protocol</h3> <p>Connect to the PDBj FTP site (ftp://data.pdbjlc1.pdbj.org/) using your prefered FTP client in PASSIVE mode.</p> <h3>Using the rsync protocol</h3> <p>This is useful for full/partial mirroring of the PDB archive. Several entry points are provided, which can be viewed using the following command:</p> <pre class="codeQuoteBox" id="rsyncep_pdbarc"> <span class="prompt">$</span> rsync data.pdbjlc1.pdbj.org:: Welcome to PDBj FTP site. ftp Top level of pdb data ftp tree aproximately 1.3T ( <a href="https://data.pdbjlc1.pdbj.org/pub/pdb" rel="nofollow noopener" target="_blank">/pub/pdb</a> ) ftp_data Data directory within ftp archive aproximately 652G ( <a href="https://data.pdbjlc1.pdbj.org/pub/pdb/data" rel="nofollow noopener" target="_blank">/pub/pdb/data</a> ) ftp_derived Derived data directory within ftp archive aproximately 467M ( <a href="https://data.pdbjlc1.pdbj.org/pub/pdb/derived_data" rel="nofollow noopener" target="_blank">/pub/pdb/derived_data</a> ) ftp_doc Doc directory within ftp archive aproximately 391M ( <a href="https://data.pdbjlc1.pdbj.org/pub/pdb/doc" rel="nofollow noopener" target="_blank">/pub/pdb/doc</a> ) emdb Top level of emdb data ftp tree aproximately 13T ( <a href="https://data.pdbjlc1.pdbj.org/pub/emdb" rel="nofollow noopener" target="_blank">/pub/emdb</a> ) ftp_versioned Top level of pdb_versioned data ftp tree aproximately 237G ( <a href="https://data.pdbjlc1.pdbj.org/pdb_versioned" rel="nofollow noopener" target="_blank">/pdb_versioned</a> ) pdb_nextgen Top level of NextGen PDB archive tree approximately 85G ( <a href="https://data.pdbjlc1.pdbj.org/pdb_nextgen" rel="nofollow noopener" target="_blank">/pdb_nextgen</a> ) rsync Top level of PDBj FTP tree aproximately 21T ( <a href="https://data.pdbjlc1.pdbj.org/" rel="nofollow noopener" target="_blank">/</a> ) </pre> <p>To download the entry files in PDB format the following rsync command can be used:</p> <pre class="codeQuoteBox">rsync -avz --delete data.pdbjlc1.pdbj.org::ftp_data/structures/divided/pdb/ ./pdb </pre> <p>To download the entry files in PDB exchange format (mmCIF) the following rsync command can be used:</p> <pre class="codeQuoteBox">rsync -avz --delete data.pdbjlc1.pdbj.org::ftp_data/structures/divided/mmCIF/ ./mmCIF </pre> <p>To download the entry files in PDBML format the following rsync command can be used:</p> <pre class="codeQuoteBox">rsync -avz --delete data.pdbjlc1.pdbj.org::ftp_data/structures/divided/XML/ ./XML </pre> <p>To download the entry files in EMDB format the following rsync command can be used:</p> <pre class="codeQuoteBox">rsync -avz --delete data.pdbjlc1.pdbj.org::emdb/ ./emdb </pre> <h2>Snapshot Archive</h2> <p>The wwPDB provides a snapshot archive that contains the snapshots of the FTP archive just before the first release every year or any remediations at the wwPDB Snapshots Archive (https://s3snapshots.rcsb.org/). We provide a mirror at ftp://snapshots.pdbj.org.</p> <h3>Using the FTP protocol</h3> <p>Connect to ftp://snapshots.pdbj.org/ using your prefered FTP client in PASSIVE mode.</p> <h3>Using the rsync protocol</h3> <p>This is useful for full/partial mirroring of the shapshot archive. Several entry points are provided, which can be viewed using the following command:</p> <pre class="codeQuoteBox"> <span class="prompt">$</span> rsync snapshots.pdbj.org:: all Entire Snapshots archive 20050106 January 6, 2005 snapshot 20060103 January 3, 2006 snapshot 20070102 January 2, 2007 snapshot 20070731 July 31, 2007 snapshot 20080107 January 7, 2008 snapshot 20090105 January 5, 2009 snapshot 20090316 March 16, 2009 snapshot 20100104 January 4, 2010 snapshot 20110103 January 3, 2011 snapshot 20110707 July 7, 2011 snapshot 20120102 January 2, 2012 snapshot 20130101 January 1, 2013 snapshot 20140102 January 2, 2014 snapshot 20141203 December 3, 2014 snapshot 20150102 January 2, 2015 snapshot 20160101 January 1, 2016 snapshot 20160302 March 2, 2016 snapshot (Validation Reports Only) 20170101 January 1, 2017 snapshot 20170308 March 8, 2017 snapshot (Validation Reports Only) 20170710 July 10, 2017 snapshot 20180101 January 1, 2018 snapshot 20180321 March 21, 2018 snapshot (Validation Reports Only) 20190101 January 1, 2019 snapshot 20200101 January 1, 2020 snapshot 20200610 June 10, 2020 snapshot (Validation Reports Only) 20200722 July 22, 2020 snapshot 20200916 September 16, 2020 snapshot (Validation Reports Only) 20210105 January 5, 2021 snapshot 20220103 January 3, 2022 snapshot 20230102 January 2, 2023 snapshot 20240101 January 1, 2024 snapshot 20250101 January 1, 2025 snapshot </pre> <p>To download the shapshot from 2005-01-06 and put them in the 20050106_snapshot directory, the following command can be used:</p> <pre class="codeQuoteBox">rsync -a snapshots.pdbj.org::20050106 20050106_snapshot </pre> </div><div style="margin-left: 3em; padding-bottom: 1.25em;"><hr class="leftHR"><div style="font-size: 0.75em;"><span property="datePublished">Created: 2020-11-05</span> <span style="color: #BFBFBF;">(last edited: 1 month ago)</span><span style="display: none;" property="dateModified">2025-01-15</span></div></div></div></div></main><aside id=""></aside><footer><div 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