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
- libcif++ C++17 general purpose mmCIF and PDB parser with strict implementations of the mmCIF DDL and PDBx/mmCIF dictionary
- cif-tools a series of tools for the manipulation, analysis and conversion of mmCIF files (depends on libcif++)
- ciftools-java Implements reading and writing of CIF files (specification) as well as their efficiently encoded counterpart, called BinaryCIF.
- 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. Built upon ciftools-java, fully supporting BinaryCIF as well.
- 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
- Mol*a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data.
- PDBe Mol* wrapper around Mol*.
- RCSB PDB Mol* wrapper around Mol*.
- 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 wwPDB
- 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
- An online PDBx/mmCIF Editor
- Pointsuite A tool for generating BIOMT and CIF symmetry records for macromolecular assemblies with point and helical symmetries.
Additional specifications
