SINCRIS Software section

Contents

• What's new?
• How to use ftp?
• Advertisment
• Software for Crystallography
• Other software
• Paper on software in J. Appled Crystallography
• Searching by keyword

The editor cannot answer to technical questions about software he did not write! Please direct your questions to the authors.

What's new?

Software for cristallography

A B C D E F G H I J K L M N

O P Q R S T U V X Y Z

A

• ABSORB - Brennan-Cowan X-ray absorption, reflection and dispersion calculation
• Absorbtion package SSRL Fortran package for calculating absorption for X-Rays
• ADESH Atomistic DEfect Simulation Handler. Representation of atomic structures, surfaces, interfaces and defects. (Commercial PC-DOS, Windows)
• AMBER Assisted Model Building with Energy Refinment. Unix
• ANSIG A tool for analysis and assignment of multidimensional spectra (SGI)
• Antheprot Protein analysis software ("Analyze the Protein")
• ARITVE - Glass modelling software (Rietveld type) DOS/Windows 95
• AZARA Suite of programs to process and view NMR data

B

• BABEL - File format conversion programm
• Barton Group, LMB, Oxford software (FTP Service) - Licence is required for these
• BIOMOL software BLAST Sequence similarity measurement
• BREADTH - pc powder line broadening analysis

C

• CACTVS Chemical Computing. 2D structure editor and display and much more. (Unix).
• Camel Jockey - absorption correction programs
• CHARMM Molecular Dynamics calculations (Chemistry at HARvard Macromolecular Mechanics)
• ChemDraw for drawing chemical structures and reaction mechanisms.
• ChemDex A UK based software database for chemistry
• ChemWeb To draw molecules on the Web
• Chemistry software Network Science chemistry software database
• Ca.R.Ine - crystallography for Mac and Windows. Includes 2D and 3D visualization, stereographic projection...
• CCP4 - programs and newletters. UK site
• CCP4 - programs and newletters. USA site
• CCP14 - Powder programs of all sorts
• CIF, Crystallographic Information Files, a complete documentation from the IUCr.
• ConInspector Advanced consensus definition and recognition. All machines except MacOS
• CORINA Generation of 3D coordinates for drug-sized chemical structures of almost any kind, including compounds with large rings, metal complexes and strained cages.
• CoreSearch To identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences. Unix
• CRYSCOMP-CRYSDRAW Set of two programs for crystallographic computing and drawing. (Commercial PC-DOS)
• CrystalDesigner Computer program for building, studying and visualising all kinds of crystal structures. From Crystal Structure Design AS. MacOS (commercial)
• Crystallographica Software toolkit designed for materials scientists, Windows. (commercial)
• Crystal Office Package for solid state Teaching and Research
• CRYSTAL PALACE PC plot program of Laue patterns for crystal orientation
• CRUSH, Calculation of rigid unit mode spectrum for framework crystal structures
• CrystalDesigner, Mac program for studying inorganic crystal structures
• Crystallographic Programs for Microcomputers
• CrystalMaker - Interactive Crystallography for the Mac
• CRYSTALVIEW Software for Mac
• CSD Crystal Structure Determination package (CSD) is a program for crystal structure treatment using X-ray/neutron experimental data from either powder or single crystal. (MS-DOS and Windows)
• CVIS - ICSD display software

D

• DDMP - Difference Distance Matrix display
• DEF4 Simulation of plane wave topographs for dislocations.
• DEFW Simulation of section topographs for dislocations
• DEMON protein program suite
• DENZO and biotex Phase A
• Desktop Microscopist Useful tasks for Electron Microscopists on McIntosh
• Diamond Visual Crystal Structure Information System
• DIFRAC Single-Crystal Diffractometer Output-Conversion
• DISCUS - Diffuse Scattering and Defect-structure simulation
• DLS-76 - Baerlochers' Distance Least Squares program
• DOCK Docking of molecules. Generates many possible orientations of binding for a ligand or ligands
• DRXWin Graphical and Analytical Tools for XRD Powder Patterns. Work with files coming from several diffractometers. (Windows).
• DS - 4-circle Diffractometer Simulation

E

• Educational Software Survey from the BCA
• Entrez From Genome to Structure. The NCBI has made a major new release of Entrez available in October 1995. The new release adds graphical access to a new "genomes" division of GenBank as well as graphical views of standard Entrez sequence records. The new release also provides a database of 3- dimensional structures derived from the PDB crystallographic database. (All platforms).
• ETH Crystallography - software distribution
• EUTAX Mac Teaching and research program
• EXPHER - Software for experimental data treatment

F

• FASTA database search program for Unix, DOS and MacOS.
• Fhkl - Computation of diffraction dat (structure factors, rocking curve...) for Dynamical Theory of X-Rays
• Flex - Molecular graphics program
• FoldIt (Light) Protein Modelling and visualization Freeware. (MacOS)
• FRODO/TOM Molecular Modelling Program for IRIS

G

• GDE Genetic Data Environment. An expandable GUI for multiple sequence analysis. See CABIOS 10, 671-675 (1994)
• GeneDoc Full Featured Multiple Sequence Alignment Editor and Shading Utility. (Unix) GenomeInspector Fast large scale correlation analysis of genetic structures. Unix
• GRASP Molecular visualization and analysis program for the display and manipulation of the surfaces of molecules and their electrostatic properties. (Commercial). SGI Unix
• GSAS General Structure Analysis System

H

• HBPLUS - Hydrogen Bond Calculator
• HEAVY HEAVY and HASSP heavy atom search, refinement, and MIR/MAD phasing programs in an integrated package
• HMMER Hidden Markov model software. Structure analysis of DNA and proteins. (Unix)
• HotJava with a demonstration for crystallography from IUMSC
• Hyperchem Molecular Dynamics. Windows

I

• ILL Diffraction group software distribution: Lazy, explored, mountmo, xtal-3d, etc...
• Interprobe Software for the handling of chemical structures (commercial).
• ISIS/Draw - Chemical structure drawing program

J

• Jana - Modulated Structure Refinement program

K

• Kriber Crystallographic Computing. VMS, DOS

L

• LACE 3D 3D space Solid and Macromolecular Modeler. Windows 95
• laueX Simulation and indexation of Laue diagrams. Unix
• LAYER - Reciprocal lattice plotting programs for diffractometer data
• Lazy X-ray and neutron powder diffraction pattern generator 'Lazy PulverIx' with a nice Graphic User Interface and interactive plotting. (McIntosh and Unix)
• linkage and mapping mirror software at EBI (EMBL Outstation, Hinxton)

M

• MacroModel Integrated software for Modeling Organic and Bioorganic Molecules using Molecular Dynamics. Unix
• MacStripe Amalysis pf protein sequences for alpha-helical coiled coils. Mac OS version.
• MAIN Numerical and visual analysis, and modification of molecular data
• MatInspector Detection of consensus matches in DNA sequences All machines.
• mmCIF Macromolecular Crystallographic Information File dictionnary and software tools
• Modeller, Homology protein modelling
• MOIL-View Program for Visualization of Structure and Dynamics of Biomolecules and STO, for Computing Stochastic Paths, in Modelling of Biomolecular Structure and Mechanisms. (Unix, SGI and AIX)
• Molecular graphics packages List of avialable software
• Molecular Surface by Conelly. Available from Quantum Chemistry Program Exchange. E-mail: qcpe@ucs.indiana.edu
• Molecular Studio from VisChem
• MOLGEN Automatic structure elucidation in chemistry: generator for connectivity isomers, molecular mechanics and generator for configurational isomers. All OS.
• MOLMOL Display and analysis of macromolecular structures. Unix.
• MolScript
• Molphy Biology software mostly for Windows NT and DEC Alpha
• MolView Molecular rendering program for Macintosh
• MOLWT DOS facility for chemical calculations
• MOMO - Molecular Modelling Program
• MOOSE - a WWW based Query Tool for PDB data
• Moxgraph - optical constants software
• MULTAN88 from Molecular Structure Corporation (commercial)

N

• NABManipulation language for modelling of nucleic acids. Unix
• NAMD parallel, object-oriented molecular dynamics program designed for high performance molecular dynamics simulations of large biomolecular systems. PVM Unix
• NAOMI - for use in studying three-dimensional protein structures
• Neutron Scattering Software
• NMR NMR Educational software
• NMRFIT, Simulation of short-range Al/Si order in framework aluminosilicate mineral from Si MAS-NMR data
• Nucleic acid sequence interpretation
• Nuages Reconstructing the 3D surface of an object of which only cross-sections are available.

O

• O program information
• ORTEP ORTEP III, the Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustration
• ORTEX - Study and display of crystal structures
• Oxford Protein Programmes - Information

P

• PARST95 Fortran program for the calculation of a variety of structural parameters from x-ray coordinates
• PC Convolution educational software
• PDBTool - Macromolecular Geometry Browser and Analyzer
• PDB2VRML PDB to VRML converter for 3D examination of structures on the Web.
• Photon Scattering Software
• PIMM - a Pi-SCF-Molecular Mechanics Program
• PLUTON, PLATON and LEPAGE from Ton Spek
• POWDER CELL manipulation and visualisation of crystal structures of polycrystalline samples
• POWDER/PWCDS Indexation of Debye-Scherrer Powder diagrams
• PROCHECK - Checks the stereochemical quality of a protein structure
• PROPHET UNIX-based software for Data Analysis, Graphing, Statistics, Mathematical Modeling, and Sequence Analysis.
• ProFIT - Protein Fold Identification Tool
• PROSA - PROtein Structure Analysis
• PROTEIN program system
• PSA - Protein Sequence Analysis
• Powder Diffraction programmes (World Directory)

• Quantum Image Image Processing software. (Windows 95, Windows NT)

R

• RASMOL molecular graphics visualisation tool
• RASTER3D photorealistic molecular graphics
• RAVE, O, DEJAVU, Notes and FTP Services
• REMOS - Yamamoto's software for modulated structures - also PREMOS, MODPLT, PRJMS
• RETRIEVE - ICSD interrogation software
• Rietveld programs for dos/windows/PCs

S

• SAM Sequence Alignment and Modeling System. (Unix)
• SCARESCROW A graphics proram for the analysis and display of molecular dynamics trajectories. Unix
• SDS - Ordinary Structure Refinement Program
• SEQIO C functions which can read and write biological sequence files formatted using various file formats. Can be used to perform efficient database searches on biological databases.
• SETOR High-quality rendering of raster images of macromolecules. SGI Unix
• SEXIE - Calculation of Coordination Shells and Geometries
• SgInfo - Space group Info's - A comprehensive Collection of ANSI C Routines for the Handling of Space Group Symmetry
• SnB - Shake-and-Bake (Phase/Fourier Refinement)
• Shape - Analysis of structure and chemistry at the molecular surface
• Gives you immediate access to much of the information which is available in the International Tables for Electron Crystallography. (Windows)
• SPEC Unix tools for acquiring, analyzing and plotting data (Commercial)
• STAMP Alignement and analysis of protein 3-D structures
• STR3DI Molecular Modeling from Exorga(commercial). Windows 95
• SHELXL93 - Structure Refinement Program
• STEREOGRAMS Stereographic Pole Projections for any crystal symmetry and any orientation (PC DOS)
• STRUVIR A STRUPLO to VRML converter. STRUVIR prepares .wrl files for 3D visualization by any Internet browser equipped with a VRML plug-in. (Fortran and MS-DOS)
• Swiss-PdbViewer Macintosh application that can display PDB files

T

• Thermo Calc Software and Databases for Thermodynamic Calculations (DOS, OS@, Unix, VMS)
• Torsions - Phi-psi values from a PDB file
• TreeView Tree drawing software. (MacOs and Windows)
• Triton - Image processing by Fourier transforms and wavelets

U

• UMWEG95 - Umweganregung-pattern calculation
• UniChem Molecular Modelling. (Unix Cray)
• UnitCell, Unit cell parameter refinement from powder diffraction data

V

• Vector NTI viewer which helps applications within WWW browsers to retrieve and visualize molecule data. (Commercial but free for Academic).
• VMD 1.1 A package for the graphical display and visualization of biomolecular systems
• VOLCAL, calculation of polyhedron volume
• Voxel - Volumic representation of a series of slices

W

• WHAT IF - macromolecular modelling program by Gert Vriend
• WinFit, WinStruct and WinQ-Fac -
• WinFit, WinStruct, WinQ-Fac Software for Geology and powder diffraction
• WPDB Windows based software for exploring 3D structures of biological macromolecules as found in the PDB - Version 2-
• WULFF net software

X

• XABS2 - Empirical absorption correction program from Davis
• XCAD4Lp-correction of ENRAF-NONIUS CAD4-diffractometer data
• XLAT - Cell parameter refinement
• XmLmctep - Graphic representation of small crystallographic structures
• XMol X Window system molecule viewer and format convcerter. Unix
• X-PLOR - simulated annealing refinement
• Xraydif1, Powder diffraction simulation
• XRayView - a Teaching Aid for X-ray Crystallography
• XRDCALC - Powder diffraction simulation
• XRS - X-ray Rietveld System
• XR95 - Educational DOS software doing X-ray diffraction pattern simulation (+ Kossel), structure and vector space viewer, periodic table, tiling generator
• Xtal Package for structure resolution. Uses Ratmac Fortran preprocessor
• Xtaldraw Interactive computer graphics program that displays and manipulates ball and stick, polyhedral and thermal ellipsoid colored drawings of any crystal structure or molecule. (DOS Windows)
• XtalView - Macromolecular package
• Xtal-3D 3D crystal structures in VRML (Unix SGI and Windows).
• XYLEM Package of tools to enable to identify, extract and manipulate data from major databases such as GenBank and PIR. (Unix).

Z

• ZDS system for powder diffraction data
• Zldb system - data organization, GUI for data, and uniform interface framework
• XPMA and ZORTEPgraphics programs for PC and SGI workstations

Other software

Visualization, image acquisition and processing

• Acquisition of Images Digitization software for SGI Indy workstations.
• 2D and 3D image processing
• JAVA
  • Java Lattice Interactive macromolecular graphics
• Khoros Image processing
• NIH Image Public domain image processing and analysis program. (Mac Intosh)
• Visualization Software from Biosym (Commercial). Unix
• VRML demonstrations of Virtual Reality Modelling Language
  • ILL - Grenoble France
  • Le Mans France
  • University of Queensland

Graphics

• PGplot
• WWW graphics server A vast source for all kind of graphic software and information.

General interest

• Benchmarks for computer equipment
• available VRML browsers

Please send your comments and your suggestions to Yves Epelboin, epelboin@lmcp.jussieu.fr .