PDBx/mmCIF Software Tools
RCSB Data Extraction and Deposition Preparation Tools
- pdb_extract
– Tools and examples for extracting mmCIF data from structure determination applications (workstation/command-line version)
- PointSuite
– generate BIOMT and CIF symmetry records for macromolecular assemblies with point and helical symmetries
RCSB Data Format Conversion and Validation Tools
- MAXIT
Updated! October 11, 2024
– An application for processing and annotating of macromolecular structure data
- sf-convert standalone tool
– A format conversion standalone tool for structure factor files that supports more than a dozen file formats
- sf-convert web tool
– A format conversion web tool for structure factor files that supports more than a dozen file formats
- DCC
– A wrapper of third party packages to aid in validation of structure factors
- PDBML2CIF
– A tool for converting PDBML data files into mmCIF data files
RCSB Data Parsing Tools
- Core Wrapper
– A library that exports C++ mmCIF accessors to Python
- CIFPARSE-OBJ
– A Class Library of Access Tools for mmCIF in C++
- CIFTABLE (ISTable)
– A Class Library of Table Access Tools for mmCIF data
RCSB Dictionary and Data Management Tools
- MMCIF Dictionary Suite
Updated! January 10, 2022
– RCSB/PDB tools to parse, validate, manage PDBx/mmCIF data dictionaries
- Db Loader
Updated! December 10, 2021
– An application to load mmCIF data into relational databases and XML
Visualization Tools Supporting PDBx/mmCIF
- Jmol – Java macromolecular visualization tool
- UCSF Chimera – Extensible Molecular Modeling System
- OpenRasMol – Open source version of RasMol with mmCIF support
Other PDBx/mmCIF Software Libraries and Tools
- CCP4 MMDB – MMDB is a macromolecular coordinate library,
supporting CCP4 application such as REFMAC and COOT
- GEMMI - a C++11 macromolecular library with Python and Fortran bindings
- iotbx.cif and ucif
– Open-source C++/Python library used by Phenix for reading and writing CIF files,
incl. validation against dictionaries
- CBFLib – A
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
- Perl STAR (mmCIF) Parser – Object-oriented Perl modules to parse mmCIF data files
- BioPython – Python toolkit for computational biology (including support for mmCIF)
- PyCifRW – Python CIF read and write methods
- XML2PDB – Open-source C++ program for converting XML to PDB format
View the RCSB Data Processing Software Tools License Agreement.
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