Jmol – viewer for chemical structures in 3D

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.

The software is for students, educators, and researchers in chemistry, biochemistry, physics, and materials science.

Key Features

• 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.

Website: jmol.sourceforge.net
Support: Handbook
Developer: Jmol Development Team
License: GNU Lesser General Public License

Jmol is written in Java. Learn Java with our recommended free books and free tutorials.

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