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Jmol 12.3.8 Prerelease



 

Jmol 12.3.8 Prerelease

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Jmol 12.3.8 Prerelease Ranking & Summary

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User Review: 0 (0 times)
File size: 16.9 MB
Platform: Windows All
License: LGPL
Price: $0
Downloads: 23
Date added: 2011-12-12
Publisher: Egon Willighagen

Jmol 12.3.8 Prerelease description

Jmol 12.3.8 Prerelease is created to provide you with a simple yet effective 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.

Requirements:

  • The Jmol web browser applet may run on most browser Java Virtual Machines, including the Microsoft and Netscape 4.7* implementations of the Java 1.1 JVM. If you are running Microsoft Internet Explorer on the Windows operating system you should upgrade to the Sun Java Virtual Machine (see below). 
  • The standalone Jmol application requires Java 1.4 or higher. 
  • In all cases, if possible, installing the latest Java version from Sun is recommended. You can have it installed by visiting www.java.com and following instructions therein.  

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