wwPDB: PDBx/mmCIF Working Group

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="description" content="wwPDB: Worldwide Protein Data Bank"> <meta name="author" content="wwPDB.org"> <link rel="shortcut icon" href="/favicon.ico"> <link href="/css/bootstrap-v3.1.1.min.css" rel="stylesheet"> <link href="/tools/font-awesome-4.4.0/css/font-awesome.min.css" rel="stylesheet"> <link href="/css/wwPDB.css?v=4" rel="stylesheet"> <link href='https://fonts.googleapis.com/css?family=Exo+2:600' rel='stylesheet' type='text/css'> <link href='https://fonts.googleapis.com/css?family=Roboto:300, 400,500,700' rel='stylesheet' type='text/css'> <link href='https://fonts.googleapis.com/css?family=Petit+Formal+Script' rel='stylesheet' type='text/css'>  <script async src="https://www.googletagmanager.com/gtag/js?id=G-5ED0CQCXV6"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-5ED0CQCXV6'); </script> <title>wwPDB: PDBx/mmCIF Working Group</title> </head> <body> <nav id='wwpdb-nav' class='navbar navbar-fixed-top hidden-print'> <div class='container'> <div class='navbar-header'> <div class='pull-left wwpdb-logo'> <a class='brand hidden-desktop' href='/'> <img src='https://cdn.rcsb.org/wwpdb/img/core/wwpdb-logo.png'></a> </div> <button type='button' data-toggle='collapse' data-target='#navbar' aria-expanded='false' aria-controls='navbar' class='navbar-toggle collapsed'> <span class='sr-only'>Toggle navigation</span> <span class='icon-bar'></span> <span class='icon-bar'></span> <span class='icon-bar'></span> </button> </div> <div id='navbar' class='collapse navbar-collapse'> <ul class='nav navbar-nav pull-right'> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>Validation <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='/validation/validation-reports' >Validation Reports</a></li> <li><a href='/validation/validation-servers' >Validation Servers</a></li> <li><a href='/validation/onedep-validation-web-service-interface' >OneDep Validation API</a></li> </ul> </li> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>Deposition <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='http://deposit.wwpdb.org/deposition/' target='_blank'>Deposit Structure</a></li> <li><a href='/deposition/system-information' >System Information</a></li> <li><a href='/deposition/tutorial' >Tutorial</a></li> <li><a href='/deposition/faq' >FAQ</a></li> <li><a href='/deposition/deposition-resources' >All Deposition Resources</a></li> </ul> </li> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>Dictionaries <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='http://mmcif.wwpdb.org' target='_blank'>PDBx/mmCIF</a></li> <li><a href='/data/ccd' >Chemical Component Dictionary</a></li> <li><a href='/data/bird' >Biologically Interesting Molecule Reference Dictionary (BIRD)</a></li> </ul> </li> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>Documentation <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='/documentation/new-format-for-pdb-ids' >Extended PDB ID With 12 Characters</a></li> <li><a href='/documentation/file-format' >File Format</a></li> <li><a href='/documentation/biocuration' >Deposition & Biocuration Policies</a></li> <li><a href='/documentation/remediation' >Remediation</a></li> <li><a href='/documentation/journals' >Instructions to Journals</a></li> </ul> </li> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>Task Forces <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='/task/validation-task-forces' >Validation Task Forces</a></li> <li><a href='/task/xray' >X-Ray Validation</a></li> <li><a href='/task/nmr' >NMR Validation</a></li> <li><a href='/task/em' >EM Validation</a></li> <li><a href='/task/sas' >Small Angle Scattering (SAS)</a></li> <li><a href='/task/mmcif' >PDBx/mmCIF Working Group</a></li> <li><a href='/task/hybrid' >Hybrid/Integrative Methods</a></li> <li><a href='/task/ligand-validation-workshop' >Ligand Validation Workshop</a></li> <li><a href='/task/modelcif' >ModelCIF Working Group</a></li> </ul> </li> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>Downloads <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='/ftp/pdb-ftp-sites' >PDB Archive</a></li> <li><a href='/ftp/pdb-versioned-ftp-site' >PDB Versioned Archive</a></li> <li><a href='/ftp/pdb-nextgen-archive-site' >PDB NextGen Archive </a></li> </ul> </li> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>Statistics <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='/stats/deposition' >Deposition Statistics</a></li> <li><a href='/stats/download' >Download Statistics</a></li> </ul> </li> <li class='dropdown'> <a href='#' class='dropdown-toggle' data-toggle='dropdown'>About <b class='caret'></b></a> <ul class='dropdown-menu'> <li><a href='/about/contact' >Contact Us</a></li> <li><a href='/about/cite-us' >Cite Us</a></li> <li><a href='/about/publications' >Publications</a></li> <li><a href='/about/advisory' >Advisory Committee</a></li> <li><a href='/about/agreement' >Agreement</a></li> <li><a href='/about/outreach' >Outreach</a></li> <li><a href='/about/faq' >FAQ</a></li> <li><a href='/about/privacy' >Privacy</a></li> <li><a href='/about/usage-policies' >Usage Policies</a></li> <li><a href='/pdb50' >PDB50</a></li> </ul> </li> <li class='wwpdb-foundation-logo'><a href='http://foundation.wwpdb.org/' target='_blank'> <img src='https://cdn.rcsb.org/wwpdb/img/core/wwpdb-foundation-logo-sm.png'></a> </li> </ul> </div> </nav> <div class="container belowFold"> <div class="col-md-3 hidden-print"> <ul class='nav nav-list wwpdb-sidenav'> <li class='menu-title'>Task Forces</li> <li ><a href='/task/validation-task-forces' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Validation Task Forces</a></li> <li ><a href='/task/xray' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> X-Ray Validation</a></li> <li ><a href='/task/nmr' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> NMR Validation</a></li> <li ><a href='/task/em' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> EM Validation</a></li> <li ><a href='/task/sas' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Small Angle Scattering (SAS)</a></li> <li class='active'><a href='/task/mmcif' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDBx/mmCIF Working Group</a></li> <li ><a href='/task/hybrid' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Hybrid/Integrative Methods</a></li> <li ><a href='/task/ligand-validation-workshop' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Ligand Validation Workshop</a></li> <li ><a href='/task/modelcif' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> ModelCIF Working Group</a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <h1>PDBx/mmCIF Working Group</h1> <p>This Working Group provides guidance on dictionary content and promotes the standard among structural biology methods developers. The Working Group meets regularly with the wwPDB. </p> <h3>Members</h3> <ul> <li>Paul Adams, LBL (Phenix), Chair</li> <li>Paul Emsley, Oxford University (Coot)</li> <li>Nigel Moriarty, LBL (Phenix)</li> <li>Garib Murshudov, LMB-MRC (REFMAC)</li> <li>Gerard Bricogne, Global Phasing (BUSTER)</li> <li>Jeff Bell, Schrodinger</li> <li>Eugene Krissinel, STFC (CCP4)</li> <li>Nicholas Sauter, LBL (Phenix)</li> <li>Mike Word, OpenEye</li> <li>Rasmus Fogh, University of Cambridge (CCP4)</li> <li>John Ionides, WeNMR</li> </ul> <h3>Meetings</h3> <p>The Working Group was initially established in 2011 to enable the direct use of PDBx/mmCIF format files in the major macromolecular crystallographic software tools and to provide recommendations on format extensions required for deposition of large structures to the PDB (<a href="/news/news.php?year=2013#22-May-2013">announced May 2013</a>).</p> <p>At a September 2011 meeting held at PDBe, the wwPDB met with key software developers to discuss the limitations of the PDB file format in its ability to support data for large structures, complex chemistry, and new and hybrid experimental methods.</p> <p>Rather than designing an entirely new format, the consensus among developers was to actively switch to the PDBx/mmCIF format, particularly for use in deposition. A meeting outcome was the formation of this working group for the adoption of the PDBx/mmCIF format for deposition and as an exchange format between programs for macromolecular crystallography.</p> <p>Additional meetings and workshops have been hosted at PDBe and Rutgers.</p> <p> <a class="fancybox" rel="group" href="https://cdn.rcsb.org/wwpdb/img/task/hinxton_format_meeting.jpg"> <img class="img-responsive img-thumbnail" src="https://cdn.rcsb.org/wwpdb/img/task/hinxton_format_meeting_s.jpg" alt="Hinxton format meeting" /> </a> </p> <p> 2011 Workshop Participants </p> <p> Top row: Sameer Velankar, Paul Adams, Randy Read, Thomas Womack, John Westbrook, Gerard Kleywegt, Eugene Krissinel<br /> Middle row: John Ionides, Garib Murshudov, Helen Berman, Gerard Bricogne, Tom Oldfield<br /> Bottom row: Oliver Smart, Paul Emsley, Ralf Grosse-Kunstleve </p> <h3>Publications</h3> <p>PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology<br> John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M. Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg V. Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. Berman, Stephen K. Burley, Ezra Peisach (2022) <i>Journal of Molecular Biology</i> 434: 167599 doi: <a href="https://doi.org/10.1016/j.jmb.2022.167599" target="_new">10.1016/j.jmb.2022.167599</a></p> <p>Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)<br> Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, Helen M. Berman, John Berrisford, Gerard Bricogne, David G. Brown, Stephen K. Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas, Jeffrey C. Hoch, Yasuyo Ikegawa, Yumiko Kengaku, Eugene Krissinel, Genji Kurisu, Yuhe Liang, Dorothee Liebschner, Lora Mak, John L. Markley, Nigel W. Moriarty, Garib N. Murshudov, Martin Noble, Ezra Peisach, Irina Persikova, Billy K. Poon, Oleg V. Sobolev, Eldon L. Ulrich, Sameer Velankar, Clemens Vonrhein, John Westbrook, Marcin Wojdyr, Masashi Yokochij, Jasmine Y. Young (2019) <i>Acta Cryst.</i> D75, 451-454. doi: <a href="https://scripts.iucr.org/cgi-bin/paper?S2059798319004522" target="_blank">10.1107/S2059798319004522</a></p>  </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.pdbj.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbj.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.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> <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>  <link rel="stylesheet" href="/tools/fancybox/jquery.fancybox.css?v=2.1.5" type="text/css" media="screen" /> <script type="text/javascript" src="/tools/fancybox/jquery.fancybox.pack.js?v=2.1.5"></script> <script type="text/javascript"> $(document).ready(function() { $(".fancybox").fancybox(); }); </script>

CINXE.COM

wwPDB: PDBx/mmCIF Working Group