PDBx/mmCIF Software Resources

Software Libraries and Tools

  • py-mmcif RCSB Python based mmCIF Core Access Library replacing CIFPARSE-OBJ wrapper
  • CCP4 MMDB – MMDB is a macromolecular coordinate library, supporting CCP4 applications such as REFMAC and COOT
  • GEMMI C++11 macromolecular library with Python and Fortran bindings
  • atomium Python package to parse PDB, MMTF and mmCIF formats
  • CCIF CCP4 C++ library providing FORTRAN77 support and dictionary validation
  • iotbx.cif and ucif – C++/Python library used by Phenix for reading and writing CIF files, including dictionary validation
  • CIFPARSE-OBJ  RCSB PDB C++ library for accessing and checking PDBx/mmCIF data files and dictionaries with supporting tutorial and examples.
  • CIFPARSE-OBJ Python Wrapper  Boost/Python wrapper for RCSB PDB C++ CIFPARSE-OBJ library
  • Python PDBx   RCSB PDB Python light-weight read/write tools for PDBx/mmCIF files and dictioanaries with examples and tutorials
  • PDBeCIF  PDBe Python package to work with mmCIF formatted files including tutorial and examples.
  • readcif   a fast C++ CIF and mmCIF parser.
  • CBFLib   Library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files
  • mmLIB   Python macromolecular toolkit (including support for mmCIF)
  • BioJava mmCIF package – Java input and output methods for mmCIF
    and a tutorial for the protein structure modules
  • BioPython   Python toolkit for computational biology including support for mmCIF
  • PyCifRW Python CIF read and write methods
  • StarTools Tokenizer   Lexical analyser for STAR/CIF/mmCIF data inlcuding a JAVA implementation
  • Perl STAR (mmCIF) Parser Several object-oriented Perl modules to parse mmCIF data files
  • XML2PDB Open-source C++ program for converting XML to PDB format

Visualization Tools Supporting PDBx/mmCIF

  • PyMol a user-sponsored molecular visualization system on an open-source foundation.
  • Jmol Java macromolecular visualization tool supporting mmCIF
  • UCSF ChimeraX next-generation molecular visualization system, reads and writes mmCIF
  • UCSF Chimera molecular visualization system, reads mmCIF
  • OpenRasMol Open source version of RasMol with mmCIF support
  • Coot Crystallographic Object-Oriented Toolkit
  • CCP4mg CCP4 Molecular Graphics Package

Software Tools Developed at RCSB PDB

  • PDB_EXTRACT Tools and examples for extracting mmCIF data from structure determination applications
  • MAXIT An application for processing and annotating of macromolecular structure data including many format conversion features
  • SF-CONVERT A format conversion tool for structure factor files that supports more than a dozen file formats
  • mmCIF Dictionary Suite 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
  • DBLoader An application to load mmCIF data into relational databases and XML
  • PDBML2CIF A tool for converting PDBML data files into mmCIF data files