This is an archive copy of the SinCris component of the IUCr web site dating from 2008. For current content please visit the RESOURCES section of https://www.iucr.org.

SinCris

Crystallographic Software Database

Last updated 07.10.2009

A	B	C	D	E	F	G	H	I
J	K	L	M	N	O	P	Q	R
S	T	U	V	W	X	Y	Z	0 - 9

G [top]

GARLIC

Entered: Thu Apr 10 DFT 2003
Operating systems: Unix, Linux.
Languages: C.
Application fields: Biology, Graphics, visualization, virtual reality.
Description: Visualization of biomolecular structures.
References: http://garlic.mefos.hr/garlic/

GDE

Entered: Fri Nov 22 8:27:23 NFT 1996
Application fields: Biology.
Description: Genetic Data Environment. An expandable GUI for multiple
References: Gilbert Lab Bioinformatics Group

GENEFP

Entered: Thu Dec 28 8:27:23 NFT 20066
Operating System: Linux.

Type: Binary, shell.

Distribution: free
Application fields: Powder.
Bibliography: JAC (2006) 39, 4, 615
Description: Full-profile fitting program for Cu-target X-ray powder patterns. Determines integrated intensities and search for proper fundamental parameters. When some parameters, such as the grain size, have large uncertainties, the genetic algorithm has an advantage over conventional least-squares methods in finding the global extremum.
References: http://crystallography.zhenjie.googlepages.com/index.html

GETAREA

Entered: Thu Jul 16 10:12:57 DFT 1998
Operating systems: Unix, MacOS, Windows, .
Languages: Web interface.
Distribution: Free
Application fields: Biology.
Bibliography: Fraczkiewicz, R. and Braun, W. (1998), J. Comp. Chem., 19, 319-333.
Description: Quick calculation of solvent accessible surface area or solvation energy
References: http://www.scsb.utmb.edu/getarea/area_form.html

GETSPEC

Entered: Mon Sep 7 9:23:41 DFT 1998
Operating systems: Unix, MacOS, Windows, VMS, .
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Minerals, Powder.
Description: Calculates the symmetry operators and special positions for any setting of any space group based on the Hall space group symbol (S.R.Hall (1981) Acta Cryst, A37, 517-525). The input may also be given as a Hermann-Mauguin symbol in the setting-specific form used by the Inorganic Crystal Structure Database. The output lists the special positions with their multiplicities, site symmetries and all equivalent coordinates. Wyckoff letters are not given as they cannot be assigned algorithmically.
References: mailto:idbrown@mcmaster.ca

GID_SL

Entered: Tue Nov 18 9:26:14 NFT 1997
Operating systems: Unix, Windows, .
Type: Binary.
Languages: HTML form interface.
Distribution: Free
Application fields: Characterization, Diffraction, Materials Science, Surface.
Description: Simulates dynamical x-ray diffraction from strained crystals, multilayers, and superlattices. Applicable to any coplanar and non-coplanar Bragg-case geometry. The following structure profiles can be simulated: 1. Normal lattice strains da(z)/a; 2. Crystal polarizabilities x0(z), xh(z); 3. Interface roughness in multilayers (rms).
References: http://sergey.gmca.aps.anl.gov/GID_SL.html

GIXS

Entered: Fri May 1 10:54:55 DFT 1998
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Materials Science.
Description: Fluorescence, specular reflectivity and diffuse scattering modelization
References: http://www.bede.com/gixs.html

GLASSVIR

Entered: Wed Apr 16 8:48:45 DFT 1997
Operating systems: Windows.
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Minerals, Modelling.
Description: GLASSVIR is a program for preparing VRML-1 files for 3D visualization (on the Web or at home) of a selected atom-pair from your RMCA configuration file (.cfg). It is best suited for glasses with exclusive coordination (oxygen or fluorine atoms around a cation for instance). Output as polyhedral and wireframe renderings.
References: http://fluo.univ-lemans.fr:8001/glasses/glassvir.html

GRASP

Entered: Fri Nov 22 8:27:30 NFT 1996
Operating systems: Irix.
Distribution: Commercial
Description: Molecular visualization and analysis program
References: GRASP Home Page

GRETEP

Entered: Fri Sep 29 10:20:55 DFT 2000
Operating systems: Windows.
Type: Source.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: Part of the LMGP suite. Thermal Ellipsoids Plot Structure Viewing, Thermal Ellipsoid Plotting and analysis Software
References: http://www.ccp14.ac.uk/tutorial/lmgp/gretep.html

GRINSP

Entered: Thu Apr 14 15:20:55 DFT 2005
Operating systems: Windows.
Type: Source, Binary.
Language: Fortran
Distribution: Free
Application fields: Structures.
Description: Monte Carlo code for the prediction of inorganic structures built up from defined polyhedra. Limited to the P1 space group and to 3-, 4-, 5- and 6- vertices polyhedra connected by corner...
References: http://www.cristal.org/grinsp/

GSAS

Entered: Mon Jun 26 8:41:23 DFT 2000
Operating systems: HPUX, Irix, Windows, Linux, VMS.
Type: Binary.
Distribution: Free
Application fields: Minerals, Structure determination.
Description: Comprehensive system for the refinement of structural models to both x-ray and neutron diffraction data. The GSAS package can be used with both single-crystal and powder diffraction data (Rietveld analysis), even both simultaneously. Neutron data can be either from single-wavelength (reactor-based) instruments, or for those a bit more masochistic, time-of-flight instrumentation.
References: http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html

GSAS-Tools

Entered: Tue Jan 7 10:58:27 NFT 1997
Operating systems: Unix.
Distribution: Free
Application fields: Minerals, Structure determination, Chemistry, Powder.
Description: a simple tool to build and extract GSAS raw files
References: Index of /software/gsas_tools/

GUEST

Entered: Thu June 8 9:45:00 NFT 2007
Operating systems: Windows, Linux
Distribution: Free
Application fields: Minerals, Structure determination, Chemistry, Powder.
Bibliography: J.A.C. 40, 2007, pp583-588
Description: Developed for the solution of molecular crystal structures from powder diffraction data. In this package, a genetic algorithm is used for global optimization to search for the structural model. For more efficient calculation time, a modified Bragg R factor is used as the evaluation function for the genetic algorithm. Applications of this program for structure determination of molecular crystals from powder diffraction data are demonstrated with known and previously unknown structures. A friendly graphical user interface (GUI) is used to generate the control file and run the program.
References: chengdon@aphy.iphy.ac.cn

GULP

Entered: Mon Jan 8 9:45:00 NFT 2001
Operating systems: Unix, Irix, Cray, AIX, Solaris, OSF1, Linux, VMS.
Type: Source.
Languages: Fortran.
Distribution: Free academic
Application fields: Materials Science.
Description: General Utility Lattice Programme. Performs a variety of types of simulation on 3D periodic solids, gas phase clusters and isolated defects in a bulk material. Designed to handle both molecular solids and ionic materials through the use of the shell model.
References: http://www.ch.ic.ac.uk/gale/Research/gulp.html

Gaussian94

Entered: Thu Jan 1 1:00:00 NFT 1970
Operating systems: Cray.
Distribution: Commercial
Application fields: Chemistry.
Description: integrated system of programs used in computational chemistry to carry out ab initio, Density Functional Theory and semi-empirical calculations.
References: http://www.cray.com/PUBLIC/product-info/J90/GAUSSIAN/GAUSSIAN.html

GeneDoc

Entered: Fri Nov 22 8:27:24 NFT 1996
Operating systems: Unix.
Application fields: Biology.
Description: Full Featured Multiple Sequence Alignment Editor and
References: GeneDoc Home Page

GenomeInspector

Entered: Fri Nov 22 8:27:29 NFT 1996
Operating systems: Unix.
Application fields: Biology.
Description: Fast large scale correlation analysis of
References: AG BIODV: Software Development for Molecular Biology

Ghostscript

Entered: Fri Mar 7 20:02:09 NFT 1997
Operating systems: Unix, VMS, MacOS, Windows, .
Languages: C.
Distribution:
Application fields: Graphics, visualization, virtual reality.
Description: interpreter for Postscript, interpreter for PDF documents and C graphic library
References: Ghostscript, Ghostview and GSview

Ghostscript

Entered: Fri Mar 7 20:02:10 NFT 1997
Operating systems: Windows, .
Languages: C.
Distribution:
Application fields: Graphics, visualization, virtual reality.
Description: Postscript previewer
References: Ghostscript, Ghostview and GSview

Ghostview

Entered: Fri Mar 7 20:02:09 NFT 1997
Operating systems: Unix, VMS.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: Postscript previewer
References: Ghostscript, Ghostview and GSview

Gl_render

Entered: Mon Oct 19 9:04:55 DFT 1998
Operating systems: Irix, OSF1, Linux.
Type: Binary.
Distribution: Free
Application fields: Biology.
Description: To render crystal structure illustrations in POV-Ray (3.0) from MolScript or BobScript
References: ftp://www.hhmi.swmed.edu/pub/gl_render/

GraphEnt

Entered: Tue Mar 13 16:26:33 NFT 2001
Operating systems: Irix, Solaris, OSF1, Linux.
Type: Source, Binary.
Languages: C.
Distribution: Free
Application fields: Diffraction, Structure determination.
Bibliography: Glykos, N.M. & Kokkinidis, M. J. Appl. Cryst. (2000). 33, 982-985
Description: Attempts to automate the procedure of calculating maximum entropy maps, with emphasis on the calculation of difference Patterson functions for macromolecular crystallographic problems, while providing a useful graphical output of the current stage of the calculation. Its ASCII-based scripting language is expected to make it portable to other (non-macromolecular) types of problems as well.
References: http://Origin.imbb.forth.gr/~glykos/

Graphic files formats

Entered: Tue Jan 7 11:12:07 NFT 1997
Operating systems: .
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: These pages contain specifications for various
References: The Graphics File Format Page

H [top]

HARDPACK

Entered: Tue Jun 28 10:27:32 NFT 2005
Operating systems: MSDOS, Unix
Distribution: Free Academic
Language: Fortran 77, Binary
Application fields: Structures, Modelling
Bibliography: http://www.xray.cz/ecm-cd/ecm/abstract/all/51.htm
Description: Prediction of crystal structure of organic compounds from molecular structure only by minimization of potential energy
References: http://www.uni-ulm.de/fileadmin/website_uni_ulm/nawi.cheminfo/Dateien_von_Hr._Rudert/HARDPACK-full.zip

HBPLUS

Entered: Fri Nov 22 8:27:32 NFT 1996
Application fields: Biology.
Description: Hydrogen Bond Calculator
References: HBPLUS Home Page

HEAVY

Entered: Fri Nov 22 8:27:33 NFT 1996
Operating systems: Unix, VMS.
Distribution: Free academic
Application fields: Structure determination, Chemistry.
Description: Heavy atom search, refinement, and MIR/MAD phasing programs in an
References: /sincris-top/logiciel/prg-heavy.html

HELIX

Entered: Fri Sep 17 12:27:33 NFT 2004
Operating systems: Windows.
Distribution: Free
Application fields: Structure determination, Chemistry.
Description: Fiber structure determination. Helpful for understanding the relationship between filament structure models and their diffraction patterns. Allows the construction of simple filament models. Calculates the filament diffraction pattern for visual inspection. Allows rapid qualitative testing of different possible models for the unknown structure.
References: http://www.ccp13.ac.uk/software/program/Helix/INDEX.htm

HKL2MAP

Entered: Fri Sep 17 12:33:33 NFT 2004
Operating systems: Linux.
Language: shell script
Distribution: Free
Application fields: Structure determmination
Description: Graphical user-interface for macromolecular phasing. The current version connects several programs from the SHELX-suite to guide the user from analysing scaled diffraction data (SHELXC), via substructure solution (SHELXD) and phasing (SHELXE) to displaying an electron density map (Xfit). You need to have licenced versions of SHELXC/D/E and Xfit in the executable path of your computer.
References: http://www.ifom-ieo-campus.it/hkl2map/

HKL2POWDER

Entered: Wed Jun 20 12:37:23 DFT 2001
Operating systems: Unix, Windows.
Type: Binary.
Distribution: Free academic
Application fields: Powder.
Description: To convert your single crystal HKL data to a pseudo-powder pattern: a) to perform a powder style search-match phase identification on the data; b) to see how the single crystal data compares with a bulk powder diffraction scan; c) to use the derived powder data for indexing (due to a possible twinned cell); d) or as an indexing or general teaching exercise.
References: http://www.ccp14.ac.uk/tutorial/platon/hkl2powder.html

HMMER

Entered: Fri Nov 22 8:27:33 NFT 1996
Operating systems: Unix.
Application fields: Biology.
Description: Hidden Markov model software. Structure analysis of DNA and
References: Eddy Lab, Dept. of Genetics, Wash.U., St. Louis

Hartree-Fock-Dirac Application

Entered: Wed Feb 5 9:17:29 NFT 1997
Operating systems: Windows.
Type: Binary.
Languages: Fortran, Pascal.
Distribution: Free
Application fields: Scattering, Electron structure and X-ray scattering.
Description: The program uses self-consistent field Hartree-Fock-Dirac method, the algorithm of which was developed by I. M. Band (Leningrad Institute of Nuclear Physics) and allows: 1) to calculate electron densities of the atoms with any electron configuration and their energy spectra 2) to visualize the electron densities calculated 3) to compute atomic scattering functions for X-rays;
References: http://www.iphys.rnd.runnet.ru/home_page/kovtun

Hyperchem

Entered: Mon Jan 6 13:31:44 NFT 1997
Operating systems: Windows.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: Molecular Dynamics
References: Molecular Mechanics with HyperChem

I [top]

I2tif

Entered: Fri Nov 7 9:17:30 NFT 1997
Operating systems: Unix, Irix, OSF1, Linux, VMS.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: Mar image file to tiff converter.
References: ftp://ftp.mrc-lmb.cam.ac.uk/pub/jyl/i2tif-4.0.tar.gz

I3D

Entered: Tue Jan 7 11:19:37 NFT 1997
Operating systems: .
Application fields: Graphics, visualization, virtual reality.
Description: A VRML Browser for Engineering
References: Latest about i3D

IFO

Entered: Tue Nov 28 15:51:27 NFT 2000
Operating systems: Windows.
Type: Binary.
Languages: C++.
Distribution: Free academic
Application fields: Materials Science.
Bibliography: J.Appl.Cryst. 31 (1998) 609
Description: Program for Image-Reconstruction-Type Calculation of Atomic Distribution Functions; supplement to RAD.
References: http://www.pa.msu.edu/~petkov/software.html

IGOR Pro

Entered: Thu Dec 28 8:27:40 NFT 2006
Operating SystemsMacOS, Windows
Distribution: Commercial
Application fields: Neutron scattering
Bibliography: JAC (2006) 39, 6, 695
Description: Reduction and analysis of small-angle neutron scattering (SANS) and ultra-small-angle neutron scattering (USANS) data with graphical interface.
References: http://www.wavemetrics.com/

IL MILIONE

Entered: Thu Jun 06 8:27:40 NFT 2007
Distribution: Free for Academic Use
Application fields: Protein Structure Determination
Bibliography: J.A.C., 2007, 40, 3, pp609-613
Description: Suite of computer programs devoted to protein crystal structure determination by X-ray crystallography: (a) Ab initio phasing, via Patterson or direct methods. (b) Single or multiple isomorphous replacement, single- or multiple-wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. c) Molecular replacement.
References: http://www.ic.cnr.it/

ILL Diffraction group

Entered: Fri Nov 22 8:27:40 NFT 1996
Distribution: Free
Application fields: Minerals, Biology, Diffraction, Scattering, Materials Science, Chemistry, Structure determination.
Description: software distribution: Lazy, xplored, mountmo, xtal-3d, etc...
References: ftp://ftp.ill.fr/pub/dif

INDEXINP

Entered: Fri Nov 22 8:27:40 NFT 1996
Distribution:
Application fields: Chemistry, Minerals, Powder.
Description: Automatic generation of indexing input files, see CCP14
References: CCP14 Program Suite

INTLDM

Entered: Wed Sep 2 16:01:48 DFT 1998
Operating systems: Unix.
Type: Source.
Languages: Fortran.
Distribution: Free academic
Application fields: Diffraction.
Bibliography: J. Appl. Cryst. (1998) 31, 496-502
Description: Stand alone version of LAUEGEN to carry out the stages of processing Laue diffraction spots up to and including the integration of spot intensities.
References: http://www.dl.ac.uk/SRS/PX/jwc_laue/intldm.html

ISIS/Draw

Entered: Fri Nov 22 8:27:41 NFT 1996
Operating systems: Windows, MacOS.
Distribution: Free academic
Description: Chemical structure drawing program.
References: WELCOME TO MDL

ISODISPLACE

Entered: Thu Dec 26 9:59:17 NFT 2006
Operating systems: Windows, Unix, MacOS Distribution: Free
Application fields: structure determination, visualization

Bibliography: JAC (2006), 39,4, 607
Description: Internet tool for exploring the structural distortion modes of crystalline materials. Provides a GUI to several packages within the ISOTROPY software suite, generates distortion modes induced by irreducible representations of the parent spacegroup symmetry, and also provides an interactive Java applet for visualizing and interactively manipulating the free parameters of each mode.
References: http://stokes.byu.edu/isodisplace.html

ISOTROPY