(Translated by https://www.hiragana.jp/ )
Software Tools
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! April 21, 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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