JMOL

Overview

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs.

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.



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.
* Multi-language
o Translated into multiple languages: Catalan (ca), Czech (cs), Danish (da), Dutch (nl), Estonian (et), French (fr), German (de), Hungarian (hu), Italian (it), Korean (ko), Norwegian Bokmal (nb), Polish (pl), Portuguese (pt), Portuguese - Brazil (pt_BR), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) (in addition to the native English, en-US).
o 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.
o For up-to-date details or instructions for adding your language, see the Wiki.
* 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.


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