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Top : Software : Scientific : Chemistry : Crystallography

Highlights
Handy Disk Image Tools
There are a number of different ways of mounting an ISO image under Linux. The venerable mount command offers an easy solution. But if you need tools that offer more functionality for working with disk images, try some of the following excellent open source tools.

(Read more)
Kaspersky Anti-Virus
(commercial) Kaspersky Anti-Virus detects and block malicious programs of all types from entering your network: Internet-worms, Trojans, harmful Java and ActiveX applets and computer viruses including those specially developed for Linux.

Links:

  • ARP
    ARP is a software suite for improvement and objective interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models.
  • Caos
    Caos is a crystallographic package for crystal structure determination from single crystal diffraction data. Caos covers most of the crystallographic calculation: data reduction, intensity statistics, Fourier and Patterson synthesis, automatic Patterson solution, peaks interpretation, structure factor and least squares calculation with user defined blocked matrix, geometrical calculation, molecular display, publication tables, CIF files.
  • CCP4
    The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. They have been collected and developed under the auspices of the Collaborative Computing Project Number 4, in Protein Crystallography, supported by the UK Science and Engineering Research Council (serc) since 1979 and currently the Biotechnology and Biological Sciences Research Council (bbsrc), and coordinated at Daresbury Laboratory.
  • CNS
    Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.
  • ConQuest
    ConQuest is the primary program for searching and retrieving information from the Cambridge Structural Database (CSD). ConQuest provides a full range of text/numeric database search options, in addition to more complex search functionality including: Chemical substructure searching, Geometrical searching, and Intermolecular and non-bonded contact searching.
  • CONSCRIPT
    CONSCRIPT generates electron density isosurfaces for presentation in protein crystallography.
  • Eden
    Eden (short for Electron DENsity) implements the 'holographic' method of recovering the electron density in a crystal.
  • Espoir
    Espoir is a reverse Monte Carlo and pseudo simulated annealing code for ab initio crystal structure determination, either from "scratch" (from a completely random starting model) or by "molecule location" (analogous to the Molecule Replacement method), fitting either to the structure factors amplitudes "|Fobs|" extracted by powder diffractometry or to single crystal data (not any potential needed).
  • GAMGI
    GAMGI is a program to build, view, and analyze atomic strucures such as molecules, crystals, glasses, liquids, etc.
  • Gnome Chemistry Utils
    The Gnome Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry. They are used in both Gnome Crystal and GChemPaint.
  • GRID
    GRID is a computational procedure for determining energetically favourable binding sites on molecules of known structure. It may be used to study individual molecules such as drugs, molecular arrays such as membranes or crystals, and macromolecules such as proteins, nucleic acids, glycoproteins or polysaccharides.
  • Gromos
    GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. Its purpose is threefold: Simulation of arbitrary molecules in solution or crystalline state by the method of molecular dynamics (MD), stochastic dynamics (SD) or the path-integral method, energy minimisation of arbitrary molecules, and analysis of conformations obtained by experiment or by computer simulation.
  • gzwilling
    gzwilling is software that has matrix free integration of image plate and CCD diffraction data.
  • HKL
    HKL is a package of programs intended for the analysis of X-ray diffraction data collected from single crystals. It consists of three parts: XdisplayF for visualization of the diffraction pattern, Denzo for data reduction and integration, and Scalepack for merging and scaling of the intensities obtained by Denzo or other programs.
  • Jana2006
    Jana2006 is a system for solving and refinement of regular, modulated and composite structures from monocrystal and powder diffraction data. It is a freeware available for most UNIX workstations like FORTRAN77 and C sources.
  • LaueX
    LaueX simulates a Laue diagram, when given the orientation of the crystal and the cell parameters. When the structure of the crystal is known, the program may be used to evaluate the intensities of the Laue spots, displaying the results as spots whose size is proportional to the intensity.
  • LinGX
    LinGX attempt to provide a crystallographic GUI for several crystallographic Programs (e.g. shelxl, sir, platon, euhedral).
  • massXpert
    The massXpert software package is a mass spectrometry environment for linear (bio-) polymers. It inherits all the innovations of GNU polyxmass, as it is a port of that project to a cross-platform development environment.
  • McMaille
    McMaille indexes powder diffraction patterns by Monte Carlo and grid search.
  • ORTEP
    The Oak Ridge Thermal Ellipsoid Plot (ORTEP) program is a computer program, written in Fortran, for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites.
  • PLATON
    PLATON is a versatile SHELX97 compatible multipurpose crystallographic tool. Most PLATON features complement those available in the excellent and widely distributed 'public domain' SHELX97 package for crystal structure determination and refinement.
  • polyXmass
    The GNU polyxmass mass spectrometric software is a computer framework for mass spectrometry that was designed speci?cally for linear (bio-)polymers of any polymer chemistry (ie proteins, saccharides, nucleic acids...).
  • Quanto
    Quanto is a program for quantitative phase analysis of polycrystalline samples by means of the Rietveld method. It is devoted to automatically estimate the weight fraction of each crystalline phase in a mixture.
  • Rave
    RAVE is a suite of programs for single and multiple domain, single and multiple crystal real-space electron-density averaging. It also contains tools for the detection of secondary structure elements in macromolecular electron-density maps. The package succeeds the previous A suite.
  • SHELX
    SHELX is a set of programs for crystal structure determination from single-crystal diffraction data. Free to academics only.
  • SIMREF
    SIMREF is a structure refinement program for the simultaneous evaluation of several powder diffraction data sets and multiple phases per data set.
  • Situs
    Situs is a package for combining multi-resolution data from a variety of biophysical sources, including electron microscopy (EM), electron tomography, small-angle X-ray scattering (SAXS), and X-ray crystallography.
  • SnB
    SnB is based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. This program has been used in a routine fashion to solve difficult structures, containing as many as 1000 unique non-H atoms, that could not be solved by traditional reciprocal-space routines based on the tangent formula alone.
  • VICS-II
    VIsualization of Crystal Structures: It is a cross-platform program to visualize structure of crystals and molecules, and is part of VENUS (Visualization of Electron/NUclear densities and Structures).
  • X-UTIL
    X-UTIL is a set of utility programs intended for practising protein crystallographers.
  • XCrySDen
    XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It can run on most UNIX platforms, without any special hardware requirements.
  • XOrtep
    XOrtep is a slightly modified version of the ortep-for-sun code that was written to provide an editor/previewer combination based on Sun's OpenView toolkit.
  • Xtal
    Xtal is a package of over sixty crystallographic programs for calculations ranging from the reduction of raw diffraction intensities, to the solution, refinement and publication of crystal structures. These are applicable to X-ray, neutron and electron diffraction analyses, including charge density studies. The package contains interactive graphics tools and is available as execution modules for most common platforms.
  • XtalView
    XtalView is a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model. It runs on Sun, DEC, SGI, IBM and PC/Linux computers and takes full advantage of the modern workstation environment. It has a simple but comprehensive windows based interface.



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