wwPDB: File Format

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><a href='/documentation/new-format-for-pdb-ids' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Extended PDB ID With 12 Characters</a></li> <li class='active'><a href='/documentation/file-format' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> File Format</a></li> <li ><a href='/documentation/biocuration' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Deposition & Biocuration Policies</a></li> <li ><a href='/documentation/remediation' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Remediation</a></li> <li ><a href='/documentation/journals' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Instructions to Journals</a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <style> .collapsible { cursor: pointer; background: none; border: none; padding: 0; display: inline; } .content { display: none; padding: 10px; overflow: hidden; background-color: #f9f9f9; } </style> <script> document.addEventListener("DOMContentLoaded", function() { var coll = document.getElementsByClassName("collapsible"); for (var i = 0; i < coll.length; i++) { coll[i].addEventListener("click", function() { var content = this.nextElementSibling; if (content.style.display === "block") { content.style.display = "none"; } else { content.style.display = "block"; } }); } }); </script> <h1>File Format Documentation</h1> <ul> <li> <a href="http://mmcif.wwpdb.org" target="_blank">PDBx/mmCIF Dictionary</a> </li> <li> <a href="http://pdbml.wwpdb.org" target="_blank">PDBML/XML Schema</a> </li> <li> <a href="file-formats-and-the-pdb">About Legacy PDB File Format</a> </li> <br /> <li> <a href="http://mmcif.wwpdb.org/docs/user-guide/guide.html">PDBx/mmCIF User Guide</a> </li> <li> Legacy PDB File Format Guide – Version 3.30 (November 21, 2012) <span style="font-size:smaller">(November 21, 2012)</span> <div class="wwpdb-document-links"> <a href="https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf" target="_blank">PDF - US Letter</a> <a href="https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf" target="_blank">PDF - A4</a> <a href="file-format-content/format33/v3.3.html">HTML</a> </div> </li> <li> <a href="javascript:void(0)" class="collapsible">Previous versions of Legacy PDB File Format Guide</a> <div class="content"> <ul> <li> PDB File Format - Contents Guide Version 3.20 <span style="font-size:smaller">(September 15, 2008)</span> <div class="wwpdb-document-links"> <a href="https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v32_letter.pdf" target="_blank">PDF - US Letter</a> <a href="https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v32_A4.pdf" target="_blank">PDF - A4</a> <a href="file-format-content/format32/v3.2.html">HTML</a> </div> </li> <li> PDB File Format - Contents Guide Version 3.1 <span style="font-size:smaller">(July 19, 2007)</span> <div class="wwpdb-document-links"> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/format3.1-20080211.pdf" target="_blank">PDF</a> </div> </li> <li> PDB File Format - Contents Guide Version 3.0 <span style="font-size:smaller">(December 01, 2006)</span> <div class="wwpdb-document-links"> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/format3.0.1-dif.pdf" target="_blank">PDF</a> <a href="file-format-content/format30/index.html">HTML</a> </div> </li> <li> PDB File Format - Contents Guide Version 2.3 <span style="font-size:smaller">(July 09, 1998)</span> <div class="wwpdb-document-links"> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/format2.3-0108-us.pdf" target="_blank">PDF - US Letter</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/format2.3-0108-a4.pdf" target="_blank">PDF - A4</a> <a href="file-format-content/format23/v2.3.html">HTML</a> </div> </li> <li> The original Protein Data Bank Contents Guides were developed by the Protein Data Bank team at Brookhaven National laboratory. Historical copies are available. <div class="wwpdb-document-links"> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1972.pdf" target="_blank">PDF - 1972</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1976.pdf" target="_blank">PDF - 1976</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1978.pdf" target="_blank">PDF - 1978</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1985.pdf" target="_blank">PDF - 1985</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1989.pdf" target="_blank">PDF - 1989</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1992.pdf" target="_blank">PDF - 1992</a> </div> <div class="wwpdb-document-links"> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_Jan_1996.pdf" target="_blank">PDF - Jan 1996</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_Feb_1996.pdf" target="_blank">PDF - Feb 1996</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_Aug_1996.pdf" target="_blank">PDF - Aug 1996</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_Oct_1996.pdf" target="_blank">PDF - Oct 1996</a> <a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_Dec_1996.pdf" target="_blank">PDF - Dec 1996</a> </div> </li> <li> <div>The original PDB format was introduced in 1972 and used a line length of 132 characters plus 8 for sequencing. In 1976, a version using 72 characters plus 8 for sequencing was introduced. This 80-column format is what has commonly been called the (legacy) "PDB format". Many details were changed based on experience, with the major change from supporting both orthogonal and fractional coordinates to only orthogonal coordinates. From 1976 - 1977, new entries were processed and older entries reprocessed using the 1976 format.</div> </li> </ul> </div> </li> <p>See also F.C. Bernstein, T.F. Koetzle, G.J.B. Williams, E.F. Meyer Jr., M.D. Brice, J.R .Rodgers, O. Kennard, T. Shimanouchi and M. Tasumi (1977). Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.</p> </ul>  </div> </div> </div> <br> <footer class="footer"> <div class="container-fluid hidden-print" style="position: relative;"> <div class="row topFooter tinyPad"> <div class="ScreenLimitFooter"> <div class="col-sm-4"> <div class="smallMarginTop"> <a href="https://www.facebook.com/pages/Worldwide-PDB/223648640998643" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/facebook.png" width="24" height="24"></a> <a href="https://www.youtube.com/channel/UCgM7zpapumhWHDMV11FIz0Q" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/youtube-logo.png" width="24" height="24"></a> <a href="#"><img alt="RSS Feed for the Latest News" src="https://cdn.rcsb.org/wwpdb/img/core/rss.png" width="24" height="24"></a> <a href="mailto: info@wwpdb.org"><img src="https://cdn.rcsb.org/wwpdb/img/core/mail.png" width="24" height="24"></a> </div> <div class="smallMarginTop"> <a href="/news/news.php"> <p><a href="/news/news.php">News & Announcements</a></p> </a> </div> <div> <p><a href="https://lists.wwpdb.org/list/pdb-l.lists.wwpdb.org">Community Bulletin Board</a></p> </div> <div><a class='brand hidden-desktop' href='http://foundation.wwpdb.org/' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/core/wwpdb-foundation-logo.png" class="logoLimit smallMarginTop"></a></div> </div> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4><a class="h4-link" href="/download/downloads.php">Download Archive</a></h4> </div> <div class="smallMarginTop"> <a href="https://files.wwpdb.org/pub/pdb/">RCSB PDB</a> | <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/">PDBe</a> | <a href="https://ftp.pdbj.org/pub/pdb/">PDBj</a> <br> <a href="/download/downloads.php">Instructions</a> </div> <div class="row"> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4>Archive Snapshots</h4> </div> <div class="smallMarginTop"> <a href="https://s3snapshots.rcsb.org">RCSB PDB (https)</a> | <a href="ftp://snapshots.pdbj.org/">PDBj</a> </div> </div>  </div> </div> <div class="col-sm-3"> <h4> Cite wwPDB: </h4> <div class="smallMarginTop"> <em>Nature Structural Biology</em> <strong>10</strong>, 980 (2003)<br> <a href="http://dx.doi.org/10.1038/nsb1203-980" target="_blank">doi: 10.1038/nsb1203-980</a> <p class="tinyMarginTop"><a href="/about/publications.php">More publications</a></p> </div> </div> <div class="row" style="padding: 40px 0px 10px 10px"> <div class="col-sm-7"> <div class="tinyPad"> <h4>wwPDB Members:</h4> </div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/emdb/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/emdb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbe.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="http://bmrb.io/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/bmrb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.rcsb.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/rcsb-pdb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.pdbj.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbj.png" class="logoLimit img-responsive"></a></div> </div> <div class="col-sm-1"><br></br></div> <div class="col-sm-4"> <div class="row"> <div class="col-xs-6"> <a href='http://www.CoreTrustSeal.org' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/homepage/CoreTrustSeal-logo-transparent-small.png" class='img-responsive seal' style="border-right: 1px solid #666; padding-right: 50px"/></a> </div> <div class="col-xs-6"> <a href='https://globalbiodata.org/' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/homepage/GCBR-Logo-RGB.png" class='img-responsive seal'/></a> </div> </div> </div> </div> </div> <div class="row bottomFooter"> © wwPDB </div> </div> </footer>  <script type="text/javascript" src="/js/jquery-2.1.0.min.js"></script> <script type="text/javascript" src="/js/bootstrap-3.1.1.min.js"></script> <script type="text/javascript" src="/js/NavbarControl.js?v2"></script> <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-62256915-1', 'auto'); ga('send', 'pageview'); </script> </body> </html>

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wwPDB: File Format