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Jmol 12.1.33 Prerelease



 

Jmol 12.1.33 Prerelease

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Jmol 12.1.33 Prerelease Ranking & Summary

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User Review: 0 (0 times)
File size: 15.3 MB
Platform: Windows All
License: LGPL
Price: FREE
Downloads: 74
Date added: 2011-02-03
Publisher: Egon Willighagen

Jmol 12.1.33 Prerelease description

Jmol 12.1.33 Prerelease offers users with an effective yet beneficial tool which is designed as a open source molecule viewer  for students, educators, and researchers in chemistry and biochemistry.

Major Features:
  1. Free, open-source software licensed under the GNU Lesser General Public License
  2. Applet, Application, and Systems Integration Component
    • The JmolApplet is a web browser applet that can be integrated into web pages. It is ideal for development of web-based courseware and web-accessible chemical databases. The JmolApplet provides an upgrade path for users of the Chime plug-in.
    • The Jmol application is a standalone Java application that runs on the desktop.
    • The JmolViewer can be integrated as a component into other Java applications.
  3. Multi-language
    • Translated into multiple languages: Catalan (ca), Chinese (both zh_CN and zh_TW) Czech (cs), Dutch (nl), French (fr), German (de), Hungarian (hu), Italian (it), Korean (ko), Portuguese - Brazil (pt_BR), Spanish (es), Turkish (tr), (in addition to the native American English, en-US, and British English, en-GB).
    • Automatically adopts the language of the user's operating system, if it is among the translations available. You can change to another language if desired.
    • For up-to-date details or instructions for adding your language, see the Wiki.
  4. Cross-platform
    • Windows
    • Mac OS X
    • Linux / Unix
  5. Supports all major web browsers: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, Konqueror, IceWeasel, ...
  6. High-performance 3D rendering with no hardware requirements
  7. File formats (see also the file formats section within Jmol Wiki):
    • MOL: MDL / Elsevier / Symyx structure (classic version V2000)
    • V3000: MDL / Elsevier / Symyx structure (new version V3000)
    • SDF: MDL / Elsevier / Symyx structure (multiple models)
    • CTFile: MDL / Elsevier / Symyx chemical table (generic)
    • CIF: Crystallographic Information File - standard from the International Union of Crystallography
    • mmCIF: Macromolecular Crystallographic Information File - standard from the International Union of Crystallography
    • CML: Chemical Markup Language
    • PDB: Protein Data Bank - Research Collaboratory for Structural Bioinformatics
    • XYZ: XYZ format, XMol file - Minnesota Supercomputer Institute
    • XYZ+vib: XYZ format with added vibrational vector information
    • XYZ-FAH XYZ format for Folding@home
    • MOL2: Sybyl, Tripos
    • Alchemy Tripos
    • CSF: Fujitsu CAChe chemical structure, now Fujitsu Sygress
    • GAMESS: General Atomic and Molecular Electronic Structure System output (both US and UK variants) - Gordon Research Group, Iowa State University
    • Gaussian Gaussian 94/98/03 output - Gaussian, Inc.
    • Cube Gaussian, Inc.
    • Ghemical The Ghemical computational chemistry package
    • MM1GP Ghemical molecular mechanics file
    • HIN: HIN / HIV files from HyperChem - Hypercube, Inc.
    • Jaguar: Schrodinger, LLC
    • MOLPRO: Molpro output
    • MOPAC: MOPAC 93/97/2002 output (public domain)
    • MGF: MOPAC 2007 (v.7.101) graphf output (public domain)
    • NWCHEM: NWChem output - Pacific Northwest National Laboratory
    • odydata Odyssey data - WaveFunction, Inc.
    • xodydata Odyssey XML data - WaveFunction, Inc.
    • QOUT: Q-Chem, Inc.
    • SHELX: Structural Chemistry Department, University of Göttingen (Germany)
    • SMOL: Spartan data - Wavefunction, Inc.
    • Spinput: Spartan data - Wavefunction, Inc.
    • GRO: Gromos87 format from GROMACS
    • PQR: Modified pdb format including charge and radius
    • Amber: The Amber package of molecular simulation programs
    • JME: Java Molecular Editor - Peter Ertl
    • CASTEP The CASTEP software package, uses density functional theory
    • FHI-aims Full-potential / all-electron electronic structure theory with local orbitals - Fritz-Haber-Institut der Max-Planck-Gesellschaft
    • VASP: VASP / VAMP / Vienna ab-initio simulation package
    • DGrid: Miroslav Kohout, Max-Planck Institute
    • ADF: ADF output - Amsterdam Density Functional
    • XSD: Accelrys Materials Studio
    • AGL: ArgusLab
    • DFT:' Wien2k
    • AMPAC: AMPAC output - Semichem, Inc.
    • WebMO: WebMO interface to computational chemistry packages
    • Molden: Electron density / molecular orbitals
    • PSI3: Output files from the PSI3 suite of quantum chemical programs
    • CRYSTAL: Output files from CRYSTAL, a computational tool for solid state chemistry and physics. Theoretical Chemistry Group, Univ. Torino, Italy.
  8. Animations
  9. Vibrations
  10. Surfaces
  11. Orbitals
  12. Support for unit cell and symmetry operations
  13. Schematic shapes for secondary structures in biomolecules
  14. Measurements
    • Distance
    • Angle
    • Torsion angle
  15. Support for RasMol/Chime scripting language
  16. JavaScript support library (Jmol.js)
  17. Exports to jpg, png, gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, idtf, web page.
  18. For more details, see the history of development.
Enhancements:
  • Bug fix: CIF reader not reading files with multiple models involving GEOM_BOND
  • New feature: write xxx.OBJ -- wavefront OBJ file writing
  • New feature: isosurface MRC keyword indicates file is MRC type (for nonstandard MRC files)
  • Bug fix: scriptlevelmax 20 too small -- changed to 100
  • Bug fix: for/while local variables improperly localized in iterative functions
  • Bug fix: 12.1.32 should not have changed + to be
Requirements:
  • Java Virtual Machines,
  • Java 1.4 or higher. 

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