Application fields: bilology, macromolecular cristallography
Bibliography: JAC (2006), 39, 4, 618
Description: Facilitates the comparison of macromolecular substructures from different sources for validation purposes and to construct a consensus model containing sites from different substructures
References: http://schneider.group.ifom-ieo-campus.it/sitcom

SImPA

Entered: Wed Apr 2 9:27:12 DFT 1997
Operating systems: Windows.
Type: Binary.
Languages: C++.
Distribution: Commercial
Application fields: Characterization, Diffraction, Graphics, visualization, virtual reality, Minerals, Materials Science, Powder.
Description: SImPA(Simplified Imaging Plate Analysis / version 1.3) provides the necessary tools to process a powder X-ray diffraction image recorded on a phosphor imaging plate for further analysis as follows: (1) Image display and manipulation, e.g. pixel intensity readout, image enhancement and enlargement; (2) Sample-to-plate distance calibration for the analysis of the X-ray diffraction image; (3) Imaging plate orientation correction; (4) Removal of spurious high intensity spots (e.g. Bragg spots from large single grains); (5) Azimuthal summation of pixel intensities for the construction of a high signal-to-background intensity profile as a function of the diffraction angle. SImPA offers an easy-to-use interface. A working version of SImPA (version 1.3) is available free of charge for evaluation.
References: http://www.physics.uottawa.ca/~lpsd/simpa/simpa.htm , mailto:serge@physics.uottawa.ca

SF2CNS

Entered: Tue Jan 7 16:36:00 NFT 2003
Operating Systems: All
Languages: Fortran
Type: Source
Distribution: Free
Description: general purpose program to calculate CNS-formatted maps easily
References: sacha@lcm3b.uhp-nancy.fr

SPACER

Entered: Thu Jun 26 14:43:56 DFT 1997
Operating systems: Windows.
Languages: Turbo-Pascal.
Distribution: Free
Application fields: Topology, symmetry.
Bibliography: J. Appl. Cryst. (1997) 30, 187-181
Description: A program to display space-group information for a conventional and nonconventional coordinate system
References: mailto: kstroz@us.edu.pl

SPASM

Entered: Mon Jan 21 12:27:30 NFT 2002
Operating systems: Unix.
Type: Source.
Languages: Perl.
Application fields: Biology.
Bibliography: JAC (2002) 35,1, 137-139
Description: Tool for pattern recognition in protein structures at the level of assemblies of individual residues. See DEJAVU for the same at the level of fold. Exist as server (cgi-bin at http adresse) and program (ftp adresse).
References: http://portray.bmc.uu.se/spasm , ftp://xray.bmc.uu.se/pub/gerard/spasm

SPE

Entered: Mon Jan 6 13:20:20 NFT 1997
Operating systems: Windows.
Distribution: Free
Application fields: Topology, symmetry.
Description: Gives you immediate access to much of the information which is available in the International Tables for Electron Crystallography, on-line in your own PC.
References: mailto:max@softhard.sk

SPEC

Entered: Mon Jan 6 13:20:20 NFT 1997
Operating systems: Unix.
Distribution: Commercial
Application fields: Graphics, visualization, virtual reality.
Description: tools for acquiring, analyzing and plotting data
References: CSS home page

SPGR4D

Entered: Fri Mar 7 20:02:10 NFT 1997
Operating systems: .
Distribution: Free
Application fields: Topology, symmetry.
Bibliography: http://www.iucr.org/journals/jac
Description: acomputer program to derive (3 1)-dimensional symmetry operations from two-line symbols J. Appl. Cryst. (1997), 30, 73-78
References: mailto://fan@aphy01.iphy.ac.cn

SR5

Entered: Mon Jan 6 13:20:26 NFT 1997
Operating systems: Windows.
Distribution: Free
Application fields: Minerals, Powder, Chemistry.
Description: Rietveld program
References: FTP://ftp.minerals.csiro.au/pub/xtallography/sr5

SSM

Entered: Mon May 12 9:20:26 NFT 2003
Operating systems: Linux, SunOS, OSF
Distribution: Free academic
Application fields: Biology.
Description: Interactive service for comparing protein structures in 3D. Allows for: comparison of two structures, examination of a structure for similarity with the whole PDB or SCOP archives, best Ca-alignment of compared structures, download and visualization of best-superposed structures using RasMol (Unix/Linux platforms) or RasTop (MS Windows machines), linking the results to other services - OCA, SCOP, GeneCensus, FSSP, 3Dee, CATH, PDBSum, SWISS-PROT and ProtoMap.
References: http://www.ebi.ac.uk/msd-srv/ssm/

STAMP

Entered: Mon Jan 6 13:20:26 NFT 1997
Operating systems: .
Distribution: Free academic
Application fields: Biology.
Description: Alignement and analysis of protein 3-D structures
References: /sincris-top/logiciel/prg-stamp.html

STNET

Entered: Tue May 6 9:42:33 DFT 1997
Distribution: Free
Application fields: Chemistry, Graphics, visualization, virtual reality, Minerals, Powder, Structure, Structure determination.
Description: Drawing of Wulf nets. Part of the CCP4 suite
References: http://www.dl.ac.uk/CCP/CCP4/main.html

STOE IPDS

Entered: Wed May 6 12:50:07 DFT 1998
Operating systems: Windows.
Distribution: Commercial
Application fields: Graphics, visualization, virtual reality, Structure determination.
Description: Collection of software, from STOE, for measuring and evaluating intensities of twinned or grown-together crystals on the IPDS. Collection of images, multi-frames search, graphical representation, output (ShelX format) ...
References: http://www.stoe.com/ipdssoft.htm

STR3DI

Entered: Wes Feb 2 14:25:04 NFT 2005
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Biology, Graphics, visualization, virtual reality.
Description: Molecular modeller for organic chemists. Allows measure of every geometric parameter, examination of each atom, bond, bond length, bond angle, torsional angle, and their accompanying stereo-electronic effects, in any organic molecule.
References: http://www.exorga.com/

STRATEGY

Entered: Tue Dec 16 17:57:36 NFT 1997
Operating systems: Irix.
Type: Binary.
Distribution: Free
Application fields: Biology, Instrumentation, Structure determination.
Bibliography: J. Appl. Cryst. (1997) 30, 551-554
Description: Program to aid in data collection strategy. You can run it after indexing the first frame using DENZO. Given the space group, it determines the spindle angle to start the data collection at.
References: http://www.crystal.chem.ruu.nl/software/strategy.html

STRUCTURE TIDY

Entered: Mon Nov 16 18:23:35 NFT 1998
Operating systems: Windows.
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Structure, Crystal structure data.
Bibliography: J.Appl.Cryst. 20, 139 - 143 (1987).
Description: Crystal structure data for inorganic compounds may be standardized to avoid the confusion often encountered when comparing crystal structure data. Differing structure data of the same or an isotypic compound may be due to a different cell choice, a different unit cell origin, a rotation and/or inversion of the coordinate system and a different choice of the representative xyz triplets of the Wyckoff positions. More more details see Acta Cryst.A40, 169-183(1984), Acta Cryst.A41, 142-151(1985) and J.Alloys and Comp.197, 291-301(1993).
References: http://www.cryst.chem.uu.nl/platon/pl000415.html

STRUVIR

Entered: Mon Jan 6 13:20:31 NFT 1997
Operating systems: VMS, Windows, Unix.
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Structure determination, Chemistry, Graphics, visualization, virtual reality.
Description: A STRUPLO to VRML converter. STRUVIR prepares .wrl
References: STRUVIR

SUBGROUPGRAPH

Entered: Wed Oct 25 17:09:41 DFT 2000
Operating systems: Unix, Windows.
Type: Binary.
Languages: C++.
Distribution: Free
Application fields: Topology, symmetry.
Bibliography: J. Appl. Phys. (2000) 33, 1190
Description: Analysis of group-subgroup relations between space groups. Available both as stand alone program or through a Web interface.
References: http://www.cryst.ehu.es/sg_graph_doc.html

SURFNET

Entered: Wed Apr 1 8:57:16 DFT 1998
Operating systems: Unix.
Type: Source.
Distribution: Free academic
Application fields: Biology.
Bibliography: Laskowski R A (1995) J. Mol. Graph., 13, 323-330.
Description: Generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file.
References: http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html

SYMMOL

Entered: Tue Jan 7 16:20:00 NFT 2003
Operating systems: Unix, MacOS, Windows, VMS.
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Topology, symmetry.
Bibliography: J. Appl. Cryst (2000) 33, 2, 417
Description: Symmetrizes a group of atoms whose coordinates, either orthogonal or oblique, are given in input. It prints out informations about the given set of atoms and informations concerning its symmetry: the symmetrized orthogonal coordinates together the point group (PG), the labels and the equivalent positions. Some quantities showing the goodness-of-fit are also printed: the rms on the coordinates, the molecular rms, the maximum deviation of the coordinates of the atom from the symmetrized ones and the continuous symmetry measure (CSM) for the whole PG and for the single elements of the PG.
References: http://www.ccp14.ac.uk/ccp/web-mirrors/symmol/~pila/, http://ccp14.sims.nrc.ca/ccp/web-mirrors/symmol/~pila/, http://ccp14.semo.edu/ccp/web-mirrors/symmol/~pila/

Sacch3d

Entered: Mon Jan 27 10:59:29 NFT 1997
Operating systems: Unix, Windows, .
Languages: Java.
Distribution: Free
References: Sacch3D: Structure

Sadian91

Entered: Tue Mar 11 8:13:35 NFT 1997
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Chemistry, Structure.
Description: Sadian Searches for Atomic DIstances and ANgles in crystal structures. (W.H. Baur and D. Kassner: Sadian90 prepares input for DLS-76 (and does other things as well. Z. Krist. Suppl. Issue, No. 3, 15 (1991)))
References: ftp://ftp.minerals.csiro.au/pub/xtallography/sadian91

San Diego Benchmark

Entered: Thu Nov 14 17:52:22 NFT 1996
Distribution: Free
Application fields: .
Description: benchmark for Crystallography by the San Diego Supercomputing
References: A Crystallographic Benchmark

Scatfac

Entered: Wed Jan 31 17:38:23 NFT 2001
Operating systems: Windows.
Type: Binary.
Distribution: Free academic
Application fields: Scattering.
Description: X-ray Atomic Scattering factor display software which Can display 1 to 2 elements on the screen. can also output the data to an ASCII file
References: http://www.ccp14.ac.uk/tutorial/lmgp/scatfac.htm

Searchmatch

Entered: Wed Feb 10 8:58:59 NFT 1999
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Powder.
Description: Search match program for use with the International Centre for Diffraction Data's Powder Diffraction File: - powerful search algorithm for multi-phase identification - lightning-fast search using raw data, peak data or a combination of the two - fully integrated Boolean PDF card retrieval and display - user database, with interface to Crystallographica - fully integrated peak search and background subtraction tools - powder pattern simulation, including multi-phase mixtures - reads most common file formats - if not just ask! - writes reports directly to Microsoft Word
References: http://www.OxfordCryosystems.co.uk/index400.html

SgInfo

Entered: Tue Jan 7 11:14:21 NFT 1997
Operating systems: Unix, Windows, , MacOS.
Type: Source.
Languages: C.
Distribution: Free
Application fields: Topology, symmetry.
Description: Space group Info's - A comprehensive Collection of ANSI C
References: SgInfo - Space group Info , SgInfo - Space group Info

ShakePSD

Entered: Fri Mar 31 16:35:18 DFT 2000
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Chemistry, Structure determination.
Bibliography: J. Appl. Cryst. (2000). 33, 406-414
Description: To solve the structures of organic compounds automatically. Can discriminate whether a heavy-atom is included or not and can employ heavy-atom methods (Patterson function and search for all remaining atoms) or direct methods (tangent formula and/or minimal function).
References: mailto:kokada@rdc.ricoh.co.jp

Shape_CCMS

Entered: Mon Jan 6 13:19:13 NFT 1997
Operating systems: .
Application fields: Biology, Chemistry.
Description: Analysis of structure and chemistry at the molecular surface
References: CCMS Software--Shape

Shark frame grabber

Entered: Wed Apr 2 10:01:58 DFT 1997
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Electron microscopy.
Description: high quality digitisation of an image or diffraction pattern.
References: http://www.calidris-em.com/shark.htm

Single Crystal

Entered: Mon Apr 11 8:50:54 NFT 2005
Operating systems: MacOS.
Type: binary
Distribution: Commercial
Application fields: Diffraction, Electron Microiscopy
Description: To visualize the reciprocal lattice, simulate electron diffraction patterns and display stereographic projections. SingleCrystal reads from CrystalMaker binary files - or loads data directly from CrystalMaker via a menu command. Real-time manipulation and measurement is possible.
References: http://www.crystalmaker.com/products.html

Situs

Entered: Tue Feb 2 8:50:54 NFT 1999
Operating systems: Unix, Irix.
Type: Source.
Languages: C.
Distribution: Free
Application fields: Biology.
Bibliography: J. Structural Biology, 1999, Willy Wriggers, Ronald A. Milligan, and J. Andrew McCammon.
Description: Program package for the docking of protein crystal structures to single-molecule, low-resolution maps from electron microscopy.Developed to provide a robust and quantitative method for the localization of biomolecular subunits in low-resolution data. Use of single-molecule density maps that can be obtained by subtraction of maps from specimens of variable subunit composition. The central algorithm is a topology-representing neural network to correlate features within the structural data sets.
References: http://chemcca10.ucsd.edu/~situs/

SnB

Entered: Fri May 12 9:51:31 DFT 2000
Operating systems: Unix, Irix, AIX, OSF1, Linux.
Type: Binary.
Languages: Fortran, Java.
Distribution: Free academic
Application fields: Biology, Graphics, visualization, virtual reality, Structure determination.
Bibliography: Acta Cryst.D49, 179-181. (1993)
Description: Based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data.
References: http://www.hwi.buffalo.edu/SnB/

Space Group Explorer

Entered: Mon Jan 6 13:19:13 NFT 1997
Operating systems: Windows.
Distribution: Free
Application fields: Topology, symmetry.
Description: Gives you immediate access to much of the
References: Calidris Shareware Archive

Structure Tidy

Entered: Mon Jun 6 08:19:13 NFT 2005
Distribution: Free
Operating Systems: Unix
Application fields: structure determinatioin, topology
Description: puts crystal structures into standardized co-ordinates for comparison with other structures (to check if identical or isotypic). Available within Ton Spek's Platon (since Dec 2004)
Bibliography: E.Parthe and L.M.Gelato (1984). Acta Cryst., A40, 169-183. L.M.Gelato and E.Parthe (1987). J. Appl. Cryst. 20, 139-143. S-Z.Hu and E.Parthe (2004). Chinese J. Struct. Chem. 23, 1150-1160.
References: http://www.cryst.chem.uu.nl/platon/pl000415.html

Suites_for_small_molecules

Entered: Mon Jan 27 10:56:01 NFT 1997
Operating systems: Windows.
Distribution: Free academic
Application fields: Chemistry, Structure determination.
Description: Review on suites of programs for small molecules
References: /sincris-top/logiciel/prg-suite.html

Swiss-PdbViewer

Entered: Mon Jan 6 13:20:32 NFT 1997
Operating systems: MacOS.
Application fields: Biology, Biology.
Description: Macintosh application that can display
References: Swiss-PdbViewer Home Page

Symmet

Entered: Thu Feb 24 8:57:32 NFT 2000
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Materials Science.
Description: For the routine analysis of crystallographic texture by neutron diffraction
References: http://www.ccp14.ac.uk/ccp/web-mirrors/chalk_river_pole_figure/

T [top]

TER_SL

Entered: Mon Nov 24 9:49:04 NFT 1997
Operating systems: .
Type: Binary.
Languages: CGI Interface.
Distribution: Free
Application fields: Scattering.
Description: Calculates x-ray specular reflection from multilayers at grazing incidence. It can account for small interface roughness using Nevot and Croce's method, and the high rms roughness can be simulated with transition layers.
References: http://sergey.gmca.aps.anl.gov/TER_SL.html

TESTSYM

Entered: Mon Jan 6 13:20:33 NFT 1997
Distribution:
Application fields: Chemistry, Minerals, Powder.
Description: cell symetry checking, see CCP14.
References: CCP14 Program Suite

TOP

Entered: Mon Feb 21 19:54:02 NFT 2000
Operating systems: Unix, VMS.
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Biology.
Bibliography: J. Appl. Cryst. (2000) 33,1, 176-183 http://journals.iucr.org/j/issues/2000/01/00/mf0003/index.html
Description: Protein TOPological comparison program which detects whether there are structural similarities between two proteins.
References: http://bioinfo1.mbfys.lu.se/TOP

TOPAS-Academic

Entered: Mon Sep 27 09:26:49 NFT 2004
Operating systems: Windows.
Application fields: Chemistry, Mineralogy, Powder.
Distribution: Commercial
Description: General non-linear least squares system driven by a scripting language. Applied to solid state chemistry and optimization. Contains minimization routines wrapped by a computer algebra system; it is this foundation that makes subject dependent modules such as Rietveld refinement shine. Academic version of BRUKER-AXS TOPAS.
References: http://pws.prserv.net/Alan.Coelho/

TOPOS

Entered: Tue Jan 13 17:26:49 NFT 2004
Operating systems: Windows.
Distribution: Commercial
Application fields: Topology, symmetry.
Description: Package for calculation of geometrical and topological properties of crystal structures.
References: http://www.topos.ssu.samara.ru/

TOPXD

Entered: Thu Jan 25 12:39:19 NFT 2001
Operating systems: Unix, Irix, AIX, Solaris, OSF1, Linux.
Type: Source.
Languages: Fortran.
Distribution: Free academic
Application fields: Chemistry, X-ray charge density.
Description: Topological analysis program for experimental static electron density based on Hansen-Coppens multipole formalism
References: http://harker.chem.buffalo.edu/public/topxd/index.html

TRACER

Entered: Mon Jan 6 13:20:41 NFT 1997
Distribution:
Application fields: Chemistry, Minerals, Powder.
Description: Cell symetry checking, see CCP14.
References: CCP14 Program Suite

TRACES

Entered: Mon Jan 6 13:20:49 NFT 1997
Operating systems: Windows.
Distribution: Commercial
Application fields: Chemistry, Minerals, Powder.
Description: Powder X-ray Diffraction Software.
References: DIFFTECH - TRACES Powder X-ray Diffraction Software

TRANSQ

Entered: Fri Jun 12 17:44:30 DFT 1998
Operating systems: Unix, VMS, .
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Materials Science.
Bibliography: J. Appl. Cryst. (1996) 29, 331-340
Description: General purpose program for the simulation of white beam Laue topographs.
References: http://turquoise.lmcp.jussieu.fr/sincris-top/logiciel/transq/

TREOR90

Entered: Mon Jan 6 13:22:06 NFT 1997
Distribution:
Application fields: Chemistry, Minerals, Powder.
Description: indexing, see CCP14.
References: CCP14 Program Suite

TVtueb

Entered: Mon Jun 26 8:26:52 DFT 2000
Operating systems: Windows.
Type: Binary.
Distribution: Free academic
Application fields: Diffraction.
Description: 2D analysis of paramagentic diffuse neutron scattering data.
References: http://www.hmi.de/bereiche/N/NE/uni_tuebingen/tvtueb/tvtueb.htm

TWIN3.0

Entered: Tue May 22 17:16:55 DFT 2001
Operating systems: Windows.
Type: Binary.
Languages: Fortran.
Distribution: Free
Application fields: Topology, symmetry.
Description: The principle features of Twin3.0 for Windows are : 1.Single crystal data sets can be tested if they are subject to twinning by merohedry. 2.The volume fractions of the different twin domains can be estimated.
References: mailto:vkahlen@uni-bremen.de

TeXsan

Entered: Mon Jan 27 10:56:01 NFT 1997
Operating systems: Windows.
Distribution: Commercial
Application fields: Chemistry, Structure determination.
Description: From data processing to structure solution, modeling, refinement
References: Crystallographic Software: teXsan for Windows

TechDig

Entered: Mon Apr 12 7:45:51 DFT 1999
Operating systems: Windows.
Type: Binary.
Distribution: Shareware
Application fields: Modelling, Mathematics.
Description: Tool for digitizing data from an image of graph or plot.
References: http://www.xnet.com/~ronjones/index.html

Tessel

Entered: Thu Oct 23 14:54:02 DFT 1997
Operating systems: HPUX, Linux, VMS.
Type: Source.
Languages: Fortran.
Distribution: Free academic
Application fields: Graphics, visualization, virtual reality.
Description: Tessel2 is a 3D "compiler" to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations.
References: http://www.uniovi.es/~quimica.fisica/qcg/tessel/tessel.html

Thermo Calc

Entered: Mon Jan 6 13:20:39 NFT 1997
Operating systems: Windows, Unix, VMS, .
Application fields: Materials Science.
Description: Software and Databases for Thermodynamic Calculations
References: Thermo Calc

Torsions

Entered: Mon Jan 6 13:20:41 NFT 1997
Operating systems: Unix, Windows, VMS, .
Type: Source.
Languages: C.
Distribution: Free
Application fields: Biology.
Description: Phi-psi values from a PDB file
References: ftp://bsmcha1.biochem.ucl.ac.uk/pub/martin/torsions.c

TreeView

Entered: Mon Jan 6 13:22:05 NFT 1997
Operating systems: Windows, MacOS.
Application fields: Biology.
References: TreeView

TriMerge

Entered: Wed Apr 2 9:54:49 DFT 1997
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Electron microscopy.
Description: A full understanding of a structure can only be obtained from a three dimensional reconstruction of the structure. Our 3-dimensional programs TriMerge and TriView allow the 3-dimensional reconstruction of a structure from a tilt series of electron micrograph images, and the visualisation on the PC screen.
References: http://www.calidris-em.com/trim.htm

TriView

Entered: Wed Apr 2 9:57:09 DFT 1997
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Electron microscopy.
Description: TriView for the 3-dimensional reconstruction of a structure on a PC. TriView gives PC users access to visualisation techniques normally only available on expensive workstations, and advanced programming ensures rapid response times, even on a PC.
References: http://www.calidris-em.com/triv.htm

Triple

Entered: Thu Jan 4 15:32:38 NFT 2001
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Chemistry, Electron microscopy.
Description: direct methods of solving structures from electron. For merging and scaling full three dimensional electron diffraction data, with full treatment of crystallographic symmetry. diffraction data, with full treatment of crystallographic symmetry.
References: http://www.calidris-em.com/triple.htm

Triton

Entered: Mon Jan 6 13:39:18 NFT 1997
Operating systems: Unix.
Type: Source.
Languages: Fortran, C.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: Image processing by Fourier transforms and wavelets.
References: /sincris-top/logiciel/prg-triton.html#process

Turbo Frodo

Entered: Mon Jan 18 8:57:07 NFT 1999
Operating systems: HPUX, Irix, Linux.
Type: Binary.
Distribution: Commercial
Application fields: Biology.
Description: General purpose molecular modelling environnement to model de novo macromolecules, polypeptides as well as nucleic acids, to build such macromolecules from experimental 3-D data obtained from X-ray crystallography and NMr and to display the resulting models using various representations including Van der Waals and Connolly's molecular dot surfaces as well as spline surfaces. For Linux and HPUX use the Turbo Frodo X version.
References: http://afmb.cnrs-mrs.fr/TURBO_FRODO/

U [top]

UMWEG

Entered: Tue Jun 12 11:43:51 DFT 2001
Operating systems: Windows.
Type: Binary.
Languages: Fortran.
Distribution: Free academic
Application fields: Diffraction.
Bibliography: J.Appl. Cryst. (1999) 32, 355-361.
Description: Calculation and graphical representation of multiple diffraction patterns (Renninger-scans). Version 01.01
References: http://www.rrz.uni-hamburg.de/mpi/rossmanith/frame.html

UNISOFT

Entered: Tue Jul 10 17:57:49 DFT 2001
Operating systems: Windows.
Type: Binary.
Distribution: Free academic
Application fields: Chemistry.
Bibliography: G. Eckold, M. Stein-Arsic, H.-J. Weber, J. Appl. Crystallogr. 20 (1987) p. 134.
Description: Lattice-Dynamical Investigations. Tool for phenomenological model calculations and optimisation of experiments. Calculate and display modes of lattice vibrations
References: http://www.uni-pc.gwdg.de/eckold/uni.html

USF

Entered: Wed Jul 16 9:31:02 DFT 1997
Operating systems: Unix, VMS.
Application fields: Biology.
Description: Uppsala Software Factory. Manuals for (most of) Gerard's programs and links to other useful O or O-related information, programs and resources.
References: http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html

UWXAFS

Entered: Tue Jan 7 11:08:33 NFT 1997
Operating systems: Unix, VMS, Windows.
Type: Source.
Languages: Fortran.
Distribution: Commercial
Application fields: Materials Science, Scattering.
Description: Package for X-ray Absorption Fine Structure (XAFS)
References: UWXAFS Home Page

UXDSUM

Entered: Mon Dec 21 10:34:10 NFT 1998
Operating systems: Windows.
Type: Source, Binary.
Languages: Fortran.
Distribution: Free
Application fields: Powder.
Description: Utility for the summation of several powder patterns contained in a Bruker .uxd file. The result is also a .uxd file containing one pattern. Fortran source code included together with an example.
References: http://www.cristal.org/also.html

UnitCell

Entered: Wed May 13 10:53:09 DFT 1998
Operating systems: MacOS, Windows.
Type: Binary.
Distribution: Free
Application fields: Minerals, Powder.
Bibliography: T J B Holland and S A T Redfern (1997) Mineralogical Magazine 61: 65-77.
Description: Refines cell parameters from powder diffraction data. Unlike most existing cell refinement programs it does not require initial estimates for cell constants. Incorporates regression diagnostics.
References: http://www.esc.cam.ac.uk/astaff/holland/UnitCell.html

V [top]

VALENCE

Entered: Thu Oct 21 10:17:11 DFT 1999
Operating systems: Unix, Windows, .
Type: Source, Binary.
Languages: C.
Distribution: Free
Application fields: Biology.
Description: Calculates the bond valence given the length of a particular bond, or the bond length given the valence.
References: http://www.ccp14.ac.uk/ccp/web-mirrors/valence/

VALIST

Entered: Thu Oct 21 10:23:21 DFT 1999
Operating systems: Windows.
Type: Binary.
Languages: Visual Basic.
Distribution: Free
Application fields: Structure.
Bibliography: Brown (1996) J. Appl. Cryst. 29, 479-480
Description: Calculates bond valences for each bond listed in the input file.
References: ftp://ftp.ill.fr/pub/dif/valist

VCT

Entered: Mon Jan 6 13:22:31 NFT 1997
Operating systems: Windows.
Distribution: Free
Application fields: Minerals, Powder, Chemistry.
Description: Variable count time data colection for Rietveld refinment
References: ftp://ftp.minerals.csiro.au/pub/xtallography/sr5

VEC

Entered: Wed Nov 25 8:56:03 NFT 1998
Operating systems: Windows.
Type: Binary.
Languages: Fortran.
Distribution: Shareware
Application fields: Structure feature prediction.
Bibliography: Elements of Inorganic Structural Chemistry E.Parthé (1996) K. Sutter Parthé Pub.
Description: Makes predictions for the most probable structural features of valence compounds (Zintl phases). For a given chemical formula crystal chemical, parameters are calculated which are used to predict the average number of homonuclear bonds. Assuming that a structure with an anionic or neutral tetrahedron complex exists, these parameters serve also to select the probable base tetrahedra with which the complex can be constructed. On the screen are shown schematic drawings of the selected base tetrahedra.
References: http://www.univie.ac.at/Mineralogie/parthe2.htm

VEC-B

Entered: Tue Dec 11 17:43:16 NFT 2001
Operating systems: Windows.
Distribution: Free academic
Application fields: Electron microscopy, Graphics, visualization, virtual reality.
Description: Package for visual computing in electron crystallography. Includes: Preliminary processing of electron microscope images, Indexing and measurement of electron difffraction patterns, Determination of the defocus value from a single electron microscope image, Direct-method resolution enhancement of electron microscope images, Simulation of dynamical/kinematical electron diffraction patterns and electron microscope images, 2-, 3- and 4-dimensional FFT, 2-dimensional half-tone-graph, display of 2-, 3- and 4-dimensional Fourier maps Contour mapping of 2-dimensional patterns, Automatic determination of atomic modulation curves in an incommensurate modulated structure
References: http://cryst.iphy.ac.cn/Project/cata_program/program.html#VEC

VEGA

Entered: Mon Apr 3 12:58:47 DFT 2000
Operating systems: Unix, Irix, Windows, Linux, .
Type: Source, Binary.
Languages: C.
Distribution: Free
Application fields: Chemistry.
Description: Bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules.
References: http://users.unimi.it/~ddl

VIBRATZ

Entered: Thu Oct 21 10:11:04 DFT 1999
Operating systems: MacOS, Windows.
Type: Binary.
Distribution: Commercial
Application fields: Chemistry, Structure.
Description: Complete normal-coordinate calculation on any molecule or crystal, using traditional valence force constants and/or Urey-Bradley force constants.
References: http://www.shapesoftware.com/

VITESS

Entered: Mon May 28 11:42:55 DFT 2001
Operating systems: Solaris, Windows, OSF1, Linux.
Type: Source, Binary.
Languages: TCl/Tk.
Distribution: Free
Application fields: Instrumentation.
Description: Virtual Instrumentation Tool for Neutron Scattering at Pulsed and Continuous Sources
References: http://www.hmi.de/projects/ess/vitess/

VMD

Entered: Wed Sep 1 12:40:15 DFT 1999
Operating systems: Unix, HPUX, Irix, AIX, Solaris, Windows, OSF1, Linux.
Type: Source, Binary.
Languages: C++.
Distribution: Free
Application fields: Chemistry, Graphics, visualization, virtual reality.
Description: High performance molecular visualization program. Uses hardware accelerated 3D rendering for real-time animation of molecular dynamics trajectories as well as static structures. Can be connected with a running MD simulation for interactive simulation work.
References: http://www.ks.uiuc.edu/Research/vmd

VMRIA

Entered: Wed Oct 15 10:22:14 DFT 2003
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Powder
Description: Rietveld analysis
References: http:www.ccp14.ac.uk/web-mirrors/vmria/

VOID

Entered: Wed May 24 10:22:14 DFT 2000
Operating systems: Windows.
Type: Binary.
Distribution: Free academic
Application fields: Structure determination.
Bibliography: J. Appl. Cryst. (2000). 33, 993
Description: Provides facilities both for searching for voids, which may be part of the crystal structure or may be due to missing solvent of crystallization, and for their display
References: http://www.nuiGalway.ie/cryst/software.htm

VOLCAL

Entered: Tue Oct 3 16:49:33 DFT 2000
Operating systems: Unix, Windows.
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Structure determination.
Description: calculation of polyhedron volume
References: /sincris-top/logiciel/volcal/index.html

VRML

Entered: Thu Dec 28 13:23:51 NFT 2006
Operating systems: VRML + HTML on all machines

Distribution: Free. .

Bibliography: JAC (2006) 39,4, 620
Description: Three-dimensional general position diagrams of the superfamilies of all non-cubic magnetic space groups have been developed. The diagrams can be rotated and zoomed to aid in the visualization of the general position diagrams and include both the general positions of the atoms and the general orientations of the associated magnetic moments.

References: http://www.bk.psu.edu/faculty/litvin/Download.html

VRML Crystal Packing Visualization

Entered: Mon Jan 6 13:23:51 NFT 1997
Operating systems: Unix, Windows, MacOS.
Application fields: Structure determination, Chemistry, Teaching, Graphics, visualization, virtual reality.
Description: demonstrations of Virtual Reality Modelling Language: Crystal
References: UBC Protein Crystallography

VRML ILL

Entered: Mon Jan 6 13:32:30 NFT 1997
Operating systems: .
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Structure determination.
Description: VRML demos at ILL, France
References: ILL's Diffraction Group home page

VRML ILL Visualization

Entered: Mon Jan 6 13:24:01 NFT 1997
Operating systems: Unix, Windows, MacOS.
Application fields: Structure determination, Chemistry, Teaching, Graphics, visualization, virtual reality.
Description: demonstrations of Virtual Reality Modelling Language: ILL,
References: ILL's Diffraction Group home page

VRML Imperial College Visualization

Entered: Mon Jan 6 13:24:02 NFT 1997
Operating systems: Unix, Windows, MacOS.
Application fields: Structure determination, Chemistry, Teaching, Graphics, visualization, virtual reality.
Description: demonstrations of Virtual Reality Modelling Language: Imperial
References: VRML

VRML Le Mans

Entered: Mon Jan 6 13:32:30 NFT 1997
Operating systems: .
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Structure determination.
Description: VRML demos at Le Mans, France
References: A Crystallographer's Guide to Internet Tools and Resources - TITLE

VRML Le Mans

Entered: Mon Jan 6 13:24:07 NFT 1997
Operating systems: Unix, Windows, MacOS.
Application fields: Structure determination, Chemistry, Teaching, Graphics, visualization, virtual reality.
Description: demonstrations of Virtual Reality Modelling Language: Le Mans
References: STRUVIR

VRML Queensland

Entered: Mon Jan 6 13:32:32 NFT 1997
Operating systems: .
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Structure determination.
Description: VRML demos at University of Queensland, Australia
References: VRML 2.0: Cover page

VRML University of Queensland

Entered: Mon Jan 6 13:24:19 NFT 1997
Operating systems: Unix, Windows, MacOS.
Application fields: Structure determination, Chemistry, Teaching, Graphics, visualization, virtual reality.
Description: demonstrations of Virtual Reality Modelling Language:University of
References: VRML 2.0: Cover page

VRML guide

Entered: Fri Sep 19 8:28:00 DFT 1997
Operating systems: Unix, Windows.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: Reference guide about VRML and software using this language from the "Guide to Internet Tools and Resources" established by the IUCr
References: /iucr-top/index.html

Valmap

Entered: Mon Sep 22 8:54:35 DFT 1997
Operating systems: Windows, .
Type: Binary.
Languages: Fortran.
Distribution: Free academic
Application fields: Chemistry, Graphics, visualization, virtual reality, Minerals, Materials Science.
Bibliography: Brown, I.D. Acta Cryst. B48, 553-572. Walterson, K. Acta Cryst. A34, 901-905.
Description: A program for calculations and visualizations of contour maps of Bond Valence Sum. Version 2.1
References: mailto://jplatas@ull.es

Vector NTI

Entered: Mon Jan 6 13:22:31 NFT 1997
Operating systems: Unix, Windows.
Distribution: Free academic
Application fields: Biology, Chemistry, Structure determination.
Description: viewer which helps applications within WWW
References: InforMax, Inc.

VisualBLAST

Entered: Mon Sep 22 15:52:54 DFT 1997
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Biology.
Description: To facilitate and accelerate sequence analysis, we present, for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition, Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.
References: http://www.lmcp.jussieu.fr/~durand/HtmlDoc/software/softmain.html

VisualCrystal

Entered: Mon Sep 6 10:53:42 DFT 2004
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Mineralogy, Powder.
Description: Quantitative abalysis of XRD Powder spectra. Mathematical and statistical model, adding up the reference XRD spectrums and using the "Klug & Alexander" fundamental relation. Functionnal features: Integration and interaction of the qualitative and quantitative phase analyses, progressive reconstruction of the scan according to the ongoing phase identification, statistical characterization of the mineralogical phases of the composition, validation through chemical analysis (if available), memorization of all the elements of the analysis for later use, macro-commands for repetitive analyses and fully automated production follow-up, control and traceability, export of the mineralogical composition to the Company's Information System, multitask, multi-user(with respect of ICDD licence) and multi-language (English and French for instance).
References: http://www..visualcrystal

VisualFASTA

Entered: Mon Sep 22 15:53:42 DFT 1997
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Biology.
Description: To facilitate and accelerate sequence analysis, we present, for the first time, two easy-to-use programs designed for interactive analysis of full BLAST and FASTA output files containing protein sequence alignments. The programs, Visual BLAST and Visual FASTA, run under Microsoft Windows 95 or NT systems. They are based on the same intuitive graphical user interface (GUI) with extensive viewing, searching, editing, printing and multithreading capabilities. These programs improve the browsing of BLAST/FASTA results by offering a more convenient presentation of these results. They also implement on a computer several analytical tools which automate a manual methodology used for detailed analysis of BLAST and FASTA outputs. These tools include a pairwise sequence alignment viewer, a Hydrophobic Cluster Analysis plot alignment viewer and a tool displaying a graphical map of all database sequences aligned with the query sequence. In addition, Visual Blast includes tools for multiple sequence alignment analysis (with an amino acid patterns search engine), and Visual FASTA provides a GUI to the FASTA program.
References: http://www.lmcp.jussieu.fr/~durand/HtmlDoc/software/softmain.html

Voxel

Entered: Mon Jan 6 13:39:20 NFT 1997
Operating systems: Unix.
Type: Source.
Languages: C.
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Structure determination.
Description: Volumic representation of a series of slices
References: /sincris-top/logiciel/prg-voxel.html

W [top]

WATNCS

Entered: Mon Nov 3 9:29:48 NFT 1997
Operating systems: Irix, OSF1.
Distribution: Free
Application fields: Biology.
Description: In protein crystallographic refinement, it is quite important to avoid false water molecules instroducing noise in the electron density map. In the case that Non-crystallographic symmetry exists in the crystals, many water molecules which binds to the protein should also follow NCS as their host proteins. The WATNCS program can pick those which follow operations from all the water candidates calculated from difference fourier maps.
References: http://gamma.mbb.ki.se/~guoguang/watncs.html

WHAT IF

Entered: Mon Jan 6 13:24:19 NFT 1997
Operating systems: .
Application fields: Biology.
Description: macromolecular modelling program by Gert Vriend
References: WHAT IF

WINCELL

Entered: Wed Mar 29 8:55:48 DFT 2000
Operating systems: Windows.
Distribution: Free
Application fields: Structure determination.
Description: Unit cell refinement. Regrouping 4 interactive softwares (Win_CORREL, Win_CELREF, Win_AFMAIL et Win_CRISDR).
References: http://fazil.rajabalee.free.fr/delphi_an.htm

WULFF

Entered: Mon May 12 15:16:06 DFT 1997
Operating systems: Unix, MacOS, Windows.
Type: Source.
Languages: C.
Distribution: Free
Application fields: Minerals.
Description: Output of program "wulff.c" (ANSI C) is a Wulff Net in HP-GL A4 format. (HP-GL A4 = Hewlett Packard Graphic Language, paper size A4, i.e. 297x210mm. Most pen-plotters understand HP-GL.)
References: http://kristall.erdw.ethz.ch/software/wulff , ftp://atb.csb.yale.edu/pub/local/rwgk/wulff/

WULFFMAN

Entered: Wed Nov 22 9:28:09 NFT 2000
Operating systems: Irix, AIX, Solaris, Linux.
Type: Source, Binary.
Languages: C++.
Application fields: Topology, symmetry.
Description: Interactively examines the Wulff shapes of crystals with specified symmetries. Wulff shape is the shape that possesses the lowest surface energy for a fixed volume, and hence represents the ideal shape that the crystal would take in the absence of other constraints.
References: http://www.ctcms.nist.gov/wulffman/

WWW GID_sl

Entered: Wed May 13 9:58:40 DFT 1998
Operating systems: .
Type: Binary.
Languages: WWW interface (CGI).
Distribution: Free
Application fields: Characterization, Materials Science, Surface.
Description: A WWW interface to simulate dynamical x-ray diffraction from strained crystals, multilayers, and superlattices. Applicable to any coplanar and non-coplanar Bragg-case geometry including cases with grazing incidence and/or exit. 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

WWW TER_sl

Entered: Wed May 13 10:02:39 DFT 1998
Operating systems: .
Type: Binary.
Languages: WWW interface (CGI).
Distribution: Free
Application fields: Characterization, Materials Science, Surface.
Description: A WWW interface to calculate x-ray specular reflection from multilayers at grazing incidence. Small interface roughness can be taken into account using Nevot and Croce's method, while large rms roughness can be simulated with transition layers.
References: http://sergey.gmca.aps.anl.gov/TER_sl.html

WWW TRDS_sl

Entered: Wed May 13 10:11:46 DFT 1998
Operating systems: .
Type: Binary.
Languages: WWW interface (CGI).
Distribution: Free
Application fields: Characterization, Materials Science, Surface.
Description: A WWW interface to calculate x-ray diffuse scattering at grazing incidence from multilayers with interface roughness. Supports 9 models of interface roughness including skew roughness correlations in multilayers and scattering from atomic steps. Various angular scans can be simulated as well as 2D-maps.
References: http://sergey.gmca.aps.anl.gov/TRDS_sl.html

WYCKSPLIT

Entered: Tue Sep 15 9:07:52 DFT 1998
Operating systems: Unix, MacOS, Windows, VMS, .
Languages: C, Web interface.
Distribution: Free
Application fields: Topology, symmetry.
Bibliography: J.A.C. (1998) 31, 645
Description: Determination of the Wyckoff positions for a group-subgroup symmetry break G > H.
References: http://lcdx00.wm.lc.ehu.es/cryst/wpsplit.html

WebCT

Entered: Mon Mar 17 11:13:20 NFT 1997
Operating systems: Unix, MacOS, Windows, VMS.
Languages: Java.
Distribution: Free
Application fields: Teaching.
Description: WebCT is a tool that facilitates the creation of sophisticated World Wide Web-based educational environments. It can be used to create entire on-line courses, or to simply publish materials that supplement existing courses.
References: http://homebrew1.cs.ubc.ca/webct/

WebLab Viewer

Entered: Mon Jan 29 11:49:32 NFT 2001
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Graphics, visualization, virtual reality.
Description: Molecular graphics visualization with a full range of Windows desktop integration tools. Allows to visualize and share molecular information, build molecular models, and analyze organic and inorganic structures, proteins, DNA/RNA, and crystals.
References: http://www.msi.com/life/products/weblab/viewer/

WebEMAPS

Entered: Mon Mar 8 10:10:00 NFT 2004
Operating systems: Web.
Type: Binary, Source.
Distribution: Free Academic
Application fields: Electron Microscopy, Teaching, Diffraction
Description: Web applicatio. Simulates electron diffraction patterns and images: 1) crystal structure definition and rendering, 2) kinematic diffraction including Kikuchi and HOLZ lines, 3) Convergent beam electron diffraction by the Bloch wave method, 4) HREM image simulation by the Bloch wave method, 5) electron probe propagation and channeling, 6) structure factor and d-spacing calculations, and 7) Coherent electron diffraction. Contains a database of common crystals for materials science. Users may define their own crystals or upload a CIF file.
References: http://emaps.mrl.uiuc.edu/

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