Jmol

Jmol is an open-source Java viewer for three-dimensional chemical structures with features for chemicals, crystals, materials and biomolecules.

Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g. in chemistry and biochemistry.

Features include:

• 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
• High-performance 3D rendering with no hardware requirements
• Supports a wide range of molecular file formats:
• MOD - 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 - IN / 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 the 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
• Fully internationalised - 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

Last Updated Saturday, April 13 2013 @ 03:56 PM EDT