Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

  • The JmolApplet is a web browser applet that can be integrated into web pages.
  • The Jmol application is a standalone Java application that runs on the desktop.
  • The JmolViewer is a development tool kit that can be integrated into other Java applications.

Java-based Jmol gives you a 3D view of molecules with features for chemicals, crystals, materials and biomolecules. In addition to the downloadable version, it’s also available as a Web app or in a development tool kit. Operating System: OS Independent.

Features

  • Free, open-source software licensed under the GNU Lesser General Public License
  • 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.
  • 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.
  • Cross-platform
    • Windows
    • Mac OS X
    • Linux / Unix
  • Supports all major web browsers: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, Konqueror, IceWeasel, …
  • High-performance 3D rendering with no hardware requirements
  • 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.

    * Files which are compressed with gzip will automatically be decompressed

  • Animations
  • Vibrations
  • Surfaces
  • Orbitals
  • Support for unit cell and symmetry operations
  • Schematic shapes for secondary structures in biomolecules
  • Measurements
    • distance
    • angle
    • torsion angle
  • Support for RasMol/Chime scripting language
  • JavaScript support library (Jmol.js)
  • Exports to jpg, png, gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, idtf, web page.

To get Jmol visit jmol.sourceforge.net

Post By Gishore J Kallarackal (2,121 Posts)

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