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Overview
How to cite Jmol
What Jmol can do
Samples
Features
What the critics are saying
Obtain Jmol
Learn to use Jmol
Manuals and tutorials
Learn by example
Jmol community
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' (explanation).
If you prefer, a list of articles that describe Jmol can be found in the Jmol Literature section of the 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
- 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), Finnish (fi) French (fr), German (de), Hungarian (hu), Indonesian (id), Italian (it), Korean (ko), Malay (ms), Portuguese - Brazil (pt_BR), Spanish (es), Turkish (tr), Ukrainian (uk) (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):
* Files which are compressed with gzip will automatically be decompressed
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. - 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.
- 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. 12.2 is the latest official, stable version.
There are also prerelease versions that are being developed for enhanced functionality (odd-numbered versions like 11.7, 11.9, 12.1, 12.3).
You can get the latest stable version from this direct download link. Or, if you are interested in other versions or the prereleases, read details in the download page.
Being a .jar file, the Jmol application will be displayed as a Java icon. If you want a Jmol icon to be shown instead, you can get it from the Jmol Wiki.
Learn to use Jmol
Manuals and tutorials
A handbook has been published for learning Jmol, and there are also other publications about Jmol.
There is also a list of tutorials designed to learn the use of Jmol, and more help, within Jmol Wiki.
Finally, there is a documentation section in this web site, for more technical details.
Learn by example
You can also learn by examining web pages that use Jmol: demonstration pages within this web site, and a list of websites using Jmol in Jmol Wiki.
Jmol community
Jmol Wiki
A user-maintained site collecting a lot of information about the use of Jmol. More dynamical and frequently updated than this web site! -- visit Jmol Wiki
Mailing lists
Those with interest in molecular visualization, especially the education and research communities, are encouraged to join the jmol-users mailing list or even the jmol-developers mailing list. There you can share ideas and experiences, ask for help, give us feedback, request new features or changes, discuss implementation, submit patches, or contribute code.Without subscribing to any lists, you can also search the archives that collect all messages posted to the lists.
For more information, please visit the Project pages section.
Source : http://jmol.sourceforge.net/
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