Software for CIF and STAR

The software listed on this page includes copies of, or links to, many of the programs and libraries available for use with CIF and STAR Files. They include archival copies of software that is no longer under active development, and a snapshot of the many projects that are currently under active maintenance.


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1. General STAR File utilities

  • Star_Base STAR File validator and general-purpose access tool
  • StarDOM software package to transform data provided in the Self Defining Text Archival and Retrieval (STAR) format into XML

2. CIF validation

  • ADIT validation server for checking the format consistency of coordinates and creating validation reports about a structure before deposition in the Protein Data Bank
  • checkCIF reports on the consistency and integrity of crystal structure determinations reported in CIF format
  • CIFIO CIF input/output module of Xtal
  • CYCLOPS checks apparent data names in text files against their occurrence in one or more CIF dictionaries
  • enCIFer CIF checking, editing and visualisation software from the CCDC
  • PLATON crystallographic tool accommodating molecular geometry, molecular graphics, CIF validation and data reduction
  • publCIF CIF publishing editor, validator and formatter
  • QUASAR CIF syntax checking and file manipulation tool
  • syntax test suite (trip tests): a small collection of test files conforming (or not) to STAR/CIF syntax rules and designed as an aid to parser development
  • vcif (version 1.2) CIF syntax checker
  • vcif2 enhanced CIF syntax checker

3. Software libraries

  • CBFlib C library for accessing crystallographic binary (CBF) and image-supporting CIF (imgCIF) files
  • cciflib library for supporting the CCIF subset of mmCIF used by the CCP4 program suite
  • iotbx library for CIF input/output and validation; Python library interface and compiled (C++) parser; part of the cctbx suite
  • CIFLIB class library and C API for CIF
  • CIFPARSE C-language function library of mmCIF access tools
  • CIFPARSE-OBJ object-oriented application interface to information in mmCIF format
  • CIFtbx Fortran toolbox and dictionary checker capable of working with DDL1 and DDL2 dictionaries
  • DICT-OBJ-FILE class library of mmCIF access tools (replacing the earlier CIFOBJ class library)
  • ISTable (CIFTable) collection of classes for managing table objects
  • mmLib Python library for mmCIF and other bioinformatics applications
  • PyCifRW provides basic support for reading and writing CIF using Python
  • STAR::Parser and related Perl modules for parsing STAR compliant data files and dictionaries

4. File manipulation programs

  • cif2cif copies and pretty-prints CIFs; reformats numbers to retain standard uncertainties within defined ranges; fetches a subset of CIF according to a request list
  • CIF2CRY program for converting structural data and reflection data contained in a CIF into instructions to be read by the CRYSTALS program
  • cif2pdb converts mmCIF data sets to PDB format
  • cif2sx converts CIF files to SHELXL instruction files
  • cif2xml copies a CIF on standard input to equivalent XML on standard output
  • CIFFOLD application for folding and unfolding long lines in CIF
  • ciftex filter for translating a CIF to a TeX file
  • cifTr application program for translating files in mmCIF format into files in PDB format (from the Protein Data Bank)
  • Db Loader (mmCIF Loader) conversion of CIF data into a form loadable into a variety of relational database engines
  • DIFRAC converts diffractometer output files to CIF format
  • GSAS2CIF application to create CIFs from GSAS results (NIST web site)
  • MAXIT application for processing and annotating of macromolecular structure data (from the Protein Data Bank)
  • Open Babel open-source chemistry toolboxconverting between more than 90 chemical file formats including CIF (but without symmetry transformations)
  • OpenMMS toolkit for creating efficient representations of macromolecular structure data in several common formats
  • pdb2cif converts PDB data sets to mmCIF format
  • PDB_EXTRACT conversion of output from macromolecular structure packages to mmCIF
  • QUASAR CIF syntax checking and file manipulation tool

5. coreCIF applications

  • cif2cif copies and pretty-prints CIFs; reformats numbers to retain standard uncertainties within defined ranges; fetches a subset of CIF according to a request list
  • CIF2CRY program for converting structural data and reflection data contained in a CIF into instructions to be read by the CRYSTALS program
  • cif2sx converts CIF files to SHELXL instruction files
  • CIFEDIT is part of the ciftools package and allows viewing and editing of CIFs
  • CIFFOLD application for folding and unfolding long lines in CIF
  • CIFIO CIF input/output module of Xtal
  • CIFTAB tables for publication via (small molecule) CIF format; part of the SHELX program suite
  • CIFtbx Fortran toolbox and dictionary checker capable of working with DDL1 and DDL2 dictionaries
  • ciftex filter for translating a CIF to a TeX file
  • DIFRAC converts diffractometer output files to CIF format
  • Jmol open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules
  • PLATON crystallographic tool accommodating molecular geometry, molecular graphics, CIF validation and data reduction
  • PREPUB CIF validation module of Xtal
  • printCIF CIF typesetting service for journals of the IUCr
  • publCIF CIF publishing editor, validator and formatter
  • Xtal system of crystallographic software

6. pdCIF and msCIF applications

  • CIFEDIT is part of the ciftools package and allows viewing and editing of CIFs
  • CIFtbx Fortran toolbox and dictionary checker capable of working with DDL1 and DDL2 dictionaries
  • GSAS2CIF application to create CIFs from GSAS results (NIST web site)
  • JANA program focused on solution, refinement and interpretation of difficult, especially modulated structures
  • pdCIFplot is part of the ciftools package and allows inspection of Rietveld fits from pdCIF

7. mmCIF applications

  • ADIT deposition tool for depositing macromolecular structures in the Protein Data Bank
  • cciflib library for supporting the CCIF subset of mmCIF used by the CCP4 program suite
  • CIFLIB class library and C API for CIF
  • CIFPARSE C-language function library of mmCIF access tools
  • CIFPARSE-OBJ object-oriented application interface to information in mmCIF format
  • cifTr application program for translating files in mmCIF format into files in PDB format (from the Protein Data Bank)
  • Db Loader (mmCIF Loader) conversion of CIF data into a form loadable into a variety of relational database engines
  • DICT-OBJ-FILE class library of mmCIF access tools (replacing the earlier CIFOBJ class library)
  • ISTable (CIFTable) collection of classes for managing table objects
  • Jmol open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules
  • MAXIT application for processing and annotating of macromolecular structure data (from the Protein Data Bank)
  • mmLib Python library for mmCIF and other bioinformatics applications
  • OpenMMS toolkit for creating efficient representations of macromolecular structure data in several common formats
  • PDB_EXTRACT conversion of output from macromolecular structure packages to mmCIF
  • publBio tools and a workspace to prepare the text, experimental data tables, and figures for a structural biology or crystallization communication
  • RasMol molecular visualizer for CIF, mmCIF and other formats
  • STAR::Parser and related Perl modules for parsing STAR compliant data files and dictionaries

8. imgCIF/CBF applications

  • CBFlib C library for accessing crystallographic binary (CBF) and image-supporting CIF (imgCIF) files
  • Mosflm program for integrating single crystal diffraction data from area detectors

9. Editors with graphical user interfaces

  • CIFEDIT is part of the ciftools package and allows viewing and editing of CIFs
  • enCIFer CIF checking, editing and visualisation software from the CCDC
  • publBio tools and a workspace to prepare the text, experimental data tables, and figures for a structural biology or crystallization communication
  • publCIF CIF publishing editor, validator and formatter

10. Visualization tools

  • enCIFer CIF checking, editing and visualisation software from the CCDC
  • Jmol open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules
  • Mercury crystal structure visualisation and exploration from the CCDC
  • pdCIFplot is part of the ciftools package and allows inspection of Rietveld fits from pdCIF
  • PLATON crystallographic tool accommodating molecular geometry, molecular graphics, CIF validation and data reduction
  • RasMol molecular visualizer for CIF, mmCIF and other formats

11. Rapid development tools

  • CifSieve for enabling rapid creation of new CIF-conversant software by using a CIF dictionary as a template for input data structures

12. Obsolete or early development software

  • CIFOBJ class library of mmCIF access tools
  • CIFtbx initial version of Fortran toolbox
  • CYCLOPS initial version of CIF data name checker
  • makedict.pl and makedicthtml.pl prototype Perl applications for producing TeX and HTML formatted versions of CIF dictionaries
  • OOSTAR Object C libraries and applications for DDL1 and DDL2 compliant CIFs
  • printCIF for Word for visualizing and preparing for publication structure reports submitted to IUCr journals in Word format
  • vcif (version 0.58) CIF syntax checker
  • ZINC interface to CIF for standard Unix tools

13. Other

  • CIF++ (obsolete), CIFDOM and Jumbo components of CML (Chemical Markup Language) software
  • CIFIO CIF input/output module of Xtal
  • PREPUB CIF validation module of Xtal
  • Xtal system of crystallographic software