Home > Software > Scientific > Biology > Jmol molecule viewer

Details

Package ID

jmol

Version

14.30.2

Downloads

74968

Website

http://jmol.sourceforge.net/

Summary

An interactive viewer for three-dimensional chemical structures.

Description

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.

Features

• Free, open-source software licensed under the GNU Lesser General Public License
• Applet, Application, and Systems Integration Component*
• Multi-language
• Cross-platform
• Supports all major web browsers: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, Konqueror, IceWeasel, …
• High-performance 3D rendering with no hardware requirements
• Files which are compressed with gzip will automatically be decompressed
• Animations
• Vibrations
• Surfaces
• Orbitals
• Support for unit cell and symmetry operations
• Schematic shapes for secondary structures in biomolecules
• Measurements of 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.

Many supported 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
• 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.

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