Author Topic: Jmol is a Java molecular viewer for three-dimensional chemical structures.  (Read 2274 times)

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Jmol is a Java molecular viewer for three-dimensional chemical structures.



Quote
Jmol: an open-source Java viewer for chemical structures in 3D
with features for chemicals, crystals, materials and biomolecules
   
Overview

    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.

How to cite Jmol

    The recommended way to cite Jmol is:
    Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/

    Remember to always use uppercase 'J', lowercase 'mol' .

    If you prefer, a list of articles that describe Jmol can be found in the Jmol Literature section of Jmol Wiki.

What Jmol can do

    Samples

        Check out the Screenshot Gallery (still images) to see samples of what can be done with Jmol
        and the Demonstration pages to see buttons and menus in action (interactive applet).

    Features

            * Free, open-source software licensed under the GNU Lesser General Public License
            * Applet, Application, and Systems Integration Component
                  o 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.
                  o The Jmol application is a standalone Java application that runs on the desktop.
                  o The JmolViewer can be integrated as a component into other Java applications.
            * Cross-platform
                  o Windows
                  o Mac OS X
                  o Linux / Unix
            * Supports all major web browsers
                  o Internet Explorer (Win32)
                  o Mozilla and Firefox (Win32, OSX, Linux, Unix)
                  o Safari (Mac OS X)
                  o Opera 7.5.4 (Win32 only)
                  o Konqueror (Linux)
                  o IceWeasel (Linux)
                  o ...
            * High-performance 3D rendering with no hardware requirements
            * File formats (see also file formats section within Jmol Wiki):
                  o CIF/mmCIF - Crystallographic Information File and Macromolecular Crystallographic Information File, the standards from the International Union of Crystallography
                  o CML - Chemical Markup Language
                  o CSF - Fujitsu CAChe chemical structure, now Fujitsu Sygress
                  o CTFile - Elsevier MDL chemical table
                  o GAMESS - General Atomic and Molecular Electronic Structure System output, Gordon Research Group, Iowa State University
                  o Gaussian 94/98/03 output - Gaussian, Inc.
                  o Ghemical
                  o HIN - HyperChem from Hypercube, Inc.
                  o Jaguar - Schrodinger, LLC
                  o MM1GP - Ghemical molecular mechanics
                  o MOL - Elsevier MDL structure
                  o MOLPRO - Molpro output
                  o MOPAC - MOPAC 93/97/2002 output (public domain)
                    - MOPAC 2007 (v.7.101) graphf output (.mgf files) (public domain)
                  o NWCHEM - NWChem output, Pacific Northwest National Laboratory
                  o odydata - Odyssey data, WaveFunction, Inc.
                  o PDB - Protein Data Bank, Research Collaboratory for Structural Bioinformatics
                  o QOUT - Q-Chem, Inc.
                  o SDF - Elsevier MDL structure
                  o SHELX - Structural Chemistry Department, University of Göttingen (Germany)
                  o SMOL - Spartan data, Wavefunction, Inc.
                  o spinput - Spartan data, Wavefunction, Inc.
                  o xodydata - Odyssey XML data, WaveFunction, Inc.
                  o XYZ - Minnesota Supercomputer Institute XMol file
                  o XYZ+vib - XYZ format files with added vibrational vector information
                  o XYZ-FAH - Folding@home XYZ file
              * Files which are compressed with gzip will automatically be decompressed
            * Animations
            * Vibrations
            * Basic support for unit cell and symmetry operations
            * Schematic shapes for secondary structures in biomolecules
            * Measurements
                  o distance
                  o angle
                  o torsion angle
            * Support for RasMol/Chime scripting language
            * JavaScript support library
            * Exports to .jpg, .png, .ppm, .pdf, and PovRay
            * For more details, see the history of development.

    What the critics are saying

        Jmol v10: I can't believe it's Java!
        But it's also open-source, so there's simply no question about it.
        Get your copy now, before they run out of those virtual Java machine thingies.
        It's just in time (JIT) for Christmas, from what I hear!

            Warren L. DeLano, shell-shocked C/Python developer
            Principal Scientist, DeLano Scientific, Author of PyMOL
            December 2004.

Obtain Jmol

    Jmol v. 11.4 is the latest official, stable version.
    There are also prerelease versions that are being developed for enhanced functionality (odd-numbered versions like 11.1, 11.3, 11.5).

    You can get both the stable release and the prereleases from the download page.

http://jmol.sourceforge.net/