PDBx/mmCIF Software Resources

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Dictionaries</li> <li><a href="/dictionaries/mmcif_pdbx_v50.dic/Index">Current version (V5) PDBx/mmCIF</a></li> <li><a href="/dictionaries/mmcif_pdbx_v5_next.dic/Index">Development Version PDBx/mmCIF</a></li> <li><a href="/dictionaries/mmcif_ddl.dic/Index">Dictionary Definition Language V2</a></li> <li><a href="/dictionaries/mmcif_pdbx_vrpt.dic/Index">wwPDB Validation</a></li> <li class="divider"></li> <li class="dropdown-header">Browse Other Dictionaries</li> <li><a href="/dictionaries/mmcif_ihm_ext.dic/Index">IHMCIF</a></li> <li><a href="/dictionaries/mmcif_ihm_flr_ext.dic/Index">flrCIF</a></li> <li><a href="/dictionaries/mmcif_pdbx_v40.dic/Index">Previous PDBx/mmCIF V4</a></li> <li><a href="/dictionaries/mmcif_std.dic/Index">Original mmCIF</a></li> <li><a href="/dictionaries/mmcif_nmr-star.dic/Index">NMRIF/NMR-STAR</a></li> <li><a href="/dictionaries/mmcif_nef.dic/Index">NMR Exchange Format (NEF)</a></li> <li><a href="/dictionaries/mmcif_sas.dic/Index">SAS</a></li> <li><a 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class="row"> <h2>PDBx/mmCIF Software Resources </h2> </div> <div class="row"> <h3>Software Libraries and Tools</h3> <ul class="ul-lg"> <li><a href="https://github.com/rcsb/py-mmcif">py-mmcif</a> RCSB Python based mmCIF Core Access Library replacing CIFPARSE-OBJ wrapper</li> <li><a href="ftp://ftp.ccp4.ac.uk/mmdb/mmdb.pdf">CCP4 MMDB</a>  MMDB is a macromolecular coordinate library, supporting <a href="http://www.ccp4.ac.uk">CCP4</a> applications such as REFMAC and COOT </li> <li> <a href="http://project-gemmi.github.io/"> GEMMI </a> C++11 macromolecular library with Python and Fortran bindings </li> <li> <a href="https://github.com/PDB-REDO/libcifpp">libcif++</a> C++17 general purpose mmCIF and PDB parser with strict implementations of the mmCIF DDL and PDBx/mmCIF dictionary</li> <li> <a href="https://github.com/PDB-REDO/cif-tools">cif-tools</a> a series of tools for the manipulation, analysis and conversion of mmCIF files (depends on libcif++)</li> <li> <a href="https://github.com/rcsb/ciftools-java">ciftools-java</a> Implements reading and writing of CIF files (specification) as well as their efficiently encoded counterpart, called BinaryCIF.</li> <li> <a href="http://atomium.bioinf.org.uk">atomium</a> Python package to parse PDB, MMTF and mmCIF formats</li> <li> <a href="http://www.ccp4.ac.uk/html/cciflib.html">CCIF</a> CCP4 C++ library providing FORTRAN77 support and dictionary validation</li> <li><a href="http://cctbx.sourceforge.net/iotbx_cif/">iotbx.cif</a> and <a href="http://cctbx.sourceforge.net/ucif/">ucif</a>  C++/Python library used by <a href="http://www.phenix-online.org/">Phenix</a> for reading and writing CIF files, including dictionary validation</li> <li> <a href="http://mmcif.wwpdb.org/docs/sw-examples/cpp/html/index.html">CIFPARSE-OBJ</a>  RCSB PDB C++ library for accessing and checking PDBx/mmCIF data files and dictionaries with supporting tutorial and examples.</li> <li><a href="http://sw-tools.pdb.org/apps/CORE-WRAPPER/index.html">CIFPARSE-OBJ Python Wrapper</a>  Boost/Python wrapper for RCSB PDB C++ CIFPARSE-OBJ library </li> <li><a href="http://mmcif.wwpdb.org/docs/sw-examples/python/html/index.html"> Python PDBx</a>   RCSB PDB Python light-weight read/write tools for PDBx/mmCIF files and dictioanaries with examples and tutorials </li> <li><a href="https://pdbeurope.github.io/pdbecif">PDBeCIF</a>  PDBe Python package to work with mmCIF formatted files including tutorial and examples.</li> <li><a href="https://github.com/RBVI/readcif">readcif</a>   a fast C++ CIF and mmCIF parser.</li> <li><a href="http://sourceforge.net/projects/cbflib/">CBFLib</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/nbio/structure/io/mmcif/package-frame.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. Built upon ciftools-java, fully supporting BinaryCIF as well.</li> <li><a href="http://www.biopython.org/">BioPython</a>   Python toolkit for computational biology including <a href="http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_create_a_structure_object_from_an_mmCIF_file.3F"> support for mmCIF</a> </li> <li><a href="https://pypi.python.org/pypi/PyCifRW/4.1">PyCifRW</a> Python CIF read and write methods</li> <li><a href="http://www.globalphasing.com/startools">StarTools Tokenizer</a>   Lexical analyser for STAR/CIF/mmCIF data inlcuding a JAVA implementation</li> <li><a href="https://www.iucr.org/resources/cif/software/starparser">Perl STAR (mmCIF) Parser</a> Several object-oriented Perl modules to parse mmCIF data files</li> <li><a href="http://dunbrack.fccc.edu/xml2pdb.php">XML2PDB</a> Open-source C++ program for converting XML to PDB format</li> </ul> <h3>Visualization Tools Supporting PDBx/mmCIF</h3> <ul class="ul-lg"> <li><a href="https://github.com/molstar/molstar">Mol*</a>a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data.</li> <li><a href="https://github.com/molstar/pdbe-molstar">PDBe Mol*</a> wrapper around Mol*.</li> <li><a href="https://github.com/molstar/rcsb--molstar">RCSB PDB Mol*</a> wrapper around Mol*.</li> <li><a href="https://www.pymol.org">PyMol</a> a user-sponsored molecular visualization system on an open-source foundation. </li> <li><a href="http://jmol.sourceforge.net/">Jmol</a> Java macromolecular visualization tool supporting mmCIF</li> <li><a href="https://www.rbvi.ucsf.edu/chimerax/">UCSF ChimeraX</a> next-generation molecular visualization system, <a href=" https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats">reads</a> and <a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#formats">writes</a> mmCIF</li> <li><a href="http://plato.cgl.ucsf.edu/chimera/">UCSF Chimera</a> molecular visualization system, <a href="http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html">reads mmCIF</a></li> <li><a href="http://www.openrasmol.org/">OpenRasMol</a> Open source version of RasMol with mmCIF support</li> <li><a href="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot">Coot</a> Crystallographic Object-Oriented Toolkit </li> <li><a href="http://www.ccp4.ac.uk/MG/">CCP4mg</a> CCP4 Molecular Graphics Package </li> </ul> <h3>Software Tools Developed at wwPDB</h3> <ul class="ul-lg"> <li><a href="http://sw-tools.rcsb.org/apps/PDB_EXTRACT/index.html">PDB_EXTRACT</a> Tools and examples for extracting mmCIF data from structure determination applications</li> <li><a href="http://sw-tools.rcsb.org/apps/MAXIT/index.html">MAXIT</a> An application for processing and annotating of macromolecular structure data including many format conversion features</li> <li><a href="http://sw-tools.rcsb.org/apps/SF-CONVERT/index.html">SF-CONVERT</a> A format conversion tool for structure factor files that supports more than a dozen file formats</li> <li><a href="http://sw-tools.rcsb.org/apps/MMCIF-DICT-SUITE/index.html">mmCIF Dictionary Suite</a> Collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects</li> <li><a href="http://sw-tools.rcsb.org/apps/DB-LOADER/index.html">DBLoader</a> An application to load mmCIF data into relational databases and XML</li> <li><a href="http://sw-tools.rcsb.org/apps/PDBML2CIF/index.html">PDBML2CIF</a> A tool for converting PDBML data files into mmCIF data files</li> <li>An online <a href="https://pdbj.org/cif-editor/">PDBx/mmCIF Editor</a></li> <li><a href="https://github.com/rcsb/PointSuite">Pointsuite</a> A tool for generating BIOMT and CIF symmetry records for macromolecular assemblies with point and helical symmetries.</li> </ul> <h3>Additional specifications</h3> <ul class="ul-lg"> <li><a href="https://github.com/molstar/BinaryCIF">BinaryCIF specification</li> </ul> </div> </div>  </div>   <script src="/assets/js/jquery/core/jquery-1.11.0.min.js" ></script> <script src="/assets/css/bootstrap/js/bootstrap.js" > </script>  <script src="/js/MyApp.js"></script>   <div id="footer"> <div class="container"> <p class="muted credit">© wwPDB </p> </div> </div>  </body> </html>

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PDBx/mmCIF Software Resources