Software Tools

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <title>Software Tools</title> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <link href="/styles/general.css" rel="STYLESHEET" type="text/css"> </head> <body>  <div id="top" name="top"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr> <td width="210"><a href="http://www.rcsb.org/" target="_blank"><img alt="RCSB PDB Protein Data Bank" src="/icons-local/header/pdblogo.gif" width="198" border="0"></a></td> <td align="right" class="headertop" colspan="2" width="100%"> <a href="http://www.wwpdb.org/" target="_blank"><img alt="A Member of the wwPDB" src="/icons-local/header/wwpdb.gif" width="191" height="15" border="0"></a> <br/>An Information Portal to Biological Macromolecular Structures</td> </tr> <tr> <td style="vertical-align:top;padding-top:0.2em;"> <a href="http://www.pdb.org" class="px9 gray" target="_blank">PDB Home</a> | <a href="mailto:deposit@deposit.rcsb.org" class="px9 gray">Contact Us <img src="/icons-local/header/email.png"/></a> </td> <td style="background-image:url('/icons-local/header/header_bg2.jpg'); background-repeat: repeat-x;vertical-align:top;background-position: 0% 100%;" width="37" rowspan="2" height="33"><img src="/icons-local/spacer.gif" alt="" width="37" height="33" border="0"></td> <td style="background-image:url('/icons-local/header/header_bg3.jpg');background-repeat: repeat-x;background-color:#3333FF;background-position: 0% 100%;padding-right:2px;vertical-align:bottom;width:500px;padding-bottom:9px;" class="topnavlinks white px11" rowspan="2" valign="bottom"> <a href="/index.html" class="topnav"> Software Tools Home</a>  |  <a href="http://mmcif.pdb.org" class="topnav">Dictionary Home</a>  |  <a class="topnav" href="http://pdbml.pdb.org">PDBML Home</a> </td></tr> <tr> <td style="background-image:url('/icons-local/header/header_bg1.jpg');text-align:left;background-repeat: repeat-x;vertical-align:top;background-position: 0% 100%;"><img src="/icons-local/spacer.gif" alt="" width="37" height="13" border="0"> </td> </tr> </table> </div>  <h1>PDBx/mmCIF Software Tools</h1> <h3>RCSB Data Extraction and Deposition Preparation Tools</h3> <ul> <li><a href="https://pdb-extract.wwpdb.org">pdb_extract</a>  Tools and examples for extracting mmCIF data from structure determination applications (workstation/command-line version) <li ><a href="https://github.com/rcsb/PointSuite" target="_blank">PointSuite</a>  generate BIOMT and CIF symmetry records for macromolecular assemblies with point and helical symmetries </ul> <h3>RCSB Data Format Conversion and Validation Tools</h3> <ul> <li ><a href="/apps/MAXIT/index.html">MAXIT</a> <span class="maroon px11">Updated! October 11, 2024</span>  An application for processing and annotating of macromolecular structure data</li> </li> <li ><a href="/apps/SF-CONVERT/index.html">sf-convert standalone tool</a>   A format conversion standalone tool for structure factor files that supports more than a dozen file formats </li> <li ><a href="http://sf-tool.wwpdb.org/">sf-convert web tool</a>   A format conversion web tool for structure factor files that supports more than a dozen file formats </li> <li ><a href="/apps/DCC/index.html">DCC</a>   A wrapper of third party packages to aid in validation of structure factors </li> <li><a href="/apps/PDBML2CIF/index.html">PDBML2CIF</a>   A tool for converting PDBML data files into mmCIF data files </li> </ul> <h3>RCSB Data Parsing Tools</h3> <ul> <li ><a href="/apps/CORE-WRAPPER/index.html">Core Wrapper</a>   A library that exports C++ mmCIF accessors to Python </li> <li><a href="/apps/CIFPARSE-OBJ/index.html">CIFPARSE-OBJ</a>   A Class Library of Access Tools for mmCIF in C++ </li> </li> <li><a href="/apps/ISTABLE/index.html">CIFTABLE</a> (ISTable)  A Class Library of Table Access Tools for mmCIF data </li> </ul> <h3>RCSB Dictionary and Data Management Tools</h3> <ul> <li ><a href="/apps/MMCIF-DICT-SUITE/index.html">MMCIF Dictionary Suite</a> <span class="maroon px11">Updated! January 10, 2022</span>  RCSB/PDB tools to parse, validate, manage PDBx/mmCIF data dictionaries </li> <li><a href="/apps/DB-LOADER/index.html">Db Loader</a> <span class="maroon px11">Updated! December 10, 2021</span>  An application to load mmCIF data into relational databases and XML </li> </ul> <h3>Visualization Tools Supporting PDBx/mmCIF </h3> <ul> <li> <a href="http://jmol.sourceforge.net/">Jmol</a>  Java macromolecular visualization tool</li> <li><a href="http://plato.cgl.ucsf.edu/chimera/">UCSF Chimera </a>  Extensible Molecular Modeling System </li> <li><a href="http://www.openrasmol.org/">OpenRasMol</a>  Open source version of RasMol with mmCIF support</li> </ul> <h3>Other PDBx/mmCIF Software Libraries and Tools</h3> <ul> <li><a href="http://www.ccp4.ac.uk/cvs/viewvc.cgi/libmmdb/mmdb/">CCP4 MMDB</a>  MMDB is a macromolecular coordinate library, supporting <a href="http://www.ccp4.ac.uk">CCP4</a> application such as REFMAC and COOT </li> <li> <a href="http://project-gemmi.github.io/"> GEMMI </a> - a C++11 macromolecular library with Python and Fortran bindings </li> <li><a href="http://cctbx.sourceforge.net/iotbx_cif/">iotbx.cif</a> and <a href="http://cctbx.sourceforge.net/ucif/">ucif</a>  Open-source C++/Python library used by <a href="http://www.phenix-online.org/">Phenix</a> for reading and writing CIF files, incl. validation against dictionaries</li> <li><a href="http://www.bernstein-plus-sons.com/software/CBF">CBFLib</a>  A library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files</li> <li><a href="http://pymmlib.sourceforge.net/">mmLIB</a>  Python macromolecular toolkit (including support for mmCIF)</li> <li><a href="http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/package-summary.html"> BioJava mmCIF package</a>  Java input and output methods for mmCIF <br /> and a <a href="https://github.com/biojava/biojava3-tutorial/blob/master/structure/README.md">tutorial</a> for the protein structure modules </li> <li><a href="http://pdb.sdsc.edu/index.html#mmcif">Perl STAR (mmCIF) Parser</a>  Object-oriented Perl modules to parse mmCIF data files</li> <li><a href="http://www.biopython.org/">BioPython</a>  Python toolkit for computational biology (including support for mmCIF)</li> <li><a href="http://pycifrw.berlios.de/">PyCifRW</a>  Python CIF read and write methods</li> <li><a href="http://dunbrack.fccc.edu/xml2pdb.php">XML2PDB</a>  Open-source C++ program for converting XML to PDB format</li> </ul> <hr /> <p>View the RCSB Data Processing Software Tools <a href="/license.txt">License Agreement</a>. <p>Questions or comments? <a href="mailto:deposit@deposit.rcsb.org">Contact Us</a>.</p> <p> </p>   <div> <p> </p> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr><td class="bg9CF" colspan="3"><img src="/icons-local/spacer.gif" alt="" height="15" border="0"></td></tr> <tr><td class="bg33F right pixel11 b" colspan="3"><a class="white" href="http://www.rcsb.org/index.html" target="_blank"><i>© RCSB PDB   </i></a></td></tr> <tr><td colspan="3"><br/></td></tr> </table> </div>  </body> </html>

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Software Tools