wwPDB: Preparing PDBx/mmCIF files for Depositing Structures Large and Small

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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'>Deposition</li> <li ><a href='http://deposit.wwpdb.org/deposition/' target='_blank' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Deposit Structure</a></li> <li ><a href='/deposition/system-information' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> System Information</a></li> <li ><a href='/deposition/tutorial' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Tutorial</a></li> <li ><a href='/deposition/faq' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> FAQ</a></li> <li ><a href='/deposition/deposition-resources' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> All Deposition Resources</a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <h1>Preparing PDBx/mmCIF files for Depositing Structures</h1> <p>To better support the increasing complexity and size of data submitted to the PDB archive, the wwPDB Deposition & Biocuration system is based on the PDBx/mmCIF data dictionary and file format. The system accepts, processes and distributes PDBx/mmCIF data files.</p> <p>Depositors are encouraged to use the PDBx/mmCIF format for coordinate files whenever possible.</p> <h2 class="underline">Generating PDBx/mmCIF format files automatically</h2> <p><a href="http://mmcif.wwpdb.org/" target="_blank">PDBx/mmCIF</a> is the official working format of the wwPDB for coordinate files. It is flexible, extensible, and can accommodate structures of any size.</p> <p>PDBx/mmCIF files ready for deposition are generated by most structure refinement programs. In the event where it is not possible to use a refinement program to generate PDBx/mmCIF files, the <a href="http://pdb-extract.wwpdb.org/" target="_blank">pdb_extract</a> program may be used. <p>Additional information about the PDBx/mmCIF format can be found in <a href="http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html" target="_blank">this FAQ</a>.</p> <p>PDBx/mmCIF format is especially useful:</p> <ul> <li>When a PDBx/mmCIF file is the output of a final refinement. The developers of REFMAC, Phenix, and Buster are involved in the development of the PDBx/mmCIF format, and these programs will output PDBx/mmCIF format files that can be deposited without additional modification.</li> <li>When the structure to be deposited is large. In this context, a large structure is defined as having more than 99,999 atoms and/or more than 62 polymer chains. These are the restrictions of the traditional PDB format. PDBx/mmCIF has no atom number restriction and virtually no chain number restriction. Please consult the "Using pdb_extract" sections of this guide for more information on depositing large structures. </li> <li>When it is useful to avoid manual entry of additional information via the deposition interface. In addition to converting PDB to PDBx/mmCIF format, pdb_extract can be used to add sequence and other information to a coordinate file prior to deposition.</li> </ul> <h3>a) Refinement packages (Preferred)</h3> <p>Depositors are encouraged to use the latest version of the refinement software packages to output up-to-date and mmCIF compliant deposition files.</p> <p>Recent versions of refinement packages Phenix, REFMAC, and Buster generate PDBx/mmCIF files ready for deposition:</p> <p>Phenix: Instructions are available at the Phenix website, <a href="https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html">https://www.phenix-online.org/documentation/overviews/xray-structure-deposition.html</a></p> <p>CCP4: instructions are available for CCP4i2 (<a href="http://www.ccp4.ac.uk/deposition_ccp4i2">http://www.ccp4.ac.uk/deposition_ccp4i2</a>) or</p> <p>CCP4 Cloud (<a href="http://www.ccp4.ac.uk/deposition_ccp4cloud">http://www.ccp4.ac.uk/deposition_ccp4cloud</a>)</p> <p>REFMAC (when using outside of CCP4i2 or CCP4 Cloud): To output a PDBx/mmCIF file from REFMAC, add a card that reads "pdbout format mmcif". REFMAC can also read a file by specifying a PDBx/mmCIF file as an HKLIN argument.</p> <p>Buster: Instructions are available at the Buster website (<a href="https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif">https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif</a>)</p> <h3>b) pdb_extract</h3> <p>For non-crystallography depositions, the pdb_extract program is available as an online interface and as a standalone command-line program to convert PDB format file to PDBx/mmcif format. It extracts and harvests data in PDBx/mmCIF format from structure determination programs. To prepare PDB format data files for use with pdb_extract and the wwPDB deposition tool, please follow the instructions at <a href="/deposition/faq">OneDep FAQ</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/" 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="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/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="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>

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wwPDB: Preparing PDBx/mmCIF files for Depositing Structures Large and Small