From Egon Willighagen
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.
* 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.
o 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).
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.
o Mac OS X
o 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
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
Generally new capability
-- customizable mouse button/action bindings
-- multi-touch/Kiosk capability using SPARSHUI adaptation (U-Tube video)
-- parallel multiprocessor capability for isosurface creation
-- drag-and-drop to signed applets and the application
-- model kit mode allows rapid construction of simple models
-- extensive support for depiction of space groups
-- conversion of 2D models (SMILES, JME, MOL) to 3D
-- interface to JSDraw for 2D structure input
-- interface to Flot for plotting data
-- full implementation of Daylight SMILES/SMARTS
-- extension of Daylight SMARTS to 3D conformation
-- introduction of Jmol bioSMILES and bioSMARTS
-- new JmolSmilesApplet.jar.
-- direct reading of Uppsala electron density maps
-- natural bond orbital reading/rendering
-- direct logging to files using the LOG command