Jmol

go back to Main Page, Computational Resources, GUIS

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. It is a relatively light and fast viewer for output from various computational codes. It reads output files from ADF (molecule geometry and molecular vibrations), Gaussian, Jaguar and NWChem, amongst others. It is strictly a viewer, and the newer versions of the program cannot even save simple XYZ-coordinates of the viewed molecule (version 9 still can). The program does allow you to save jpg-pictures and it generates input-files for POVRAY so you can get publication-quality pictures. It does require SUN java 1.4 or later to be installed on the computer, it does not work properly with GNU Java.

Installation

Jmol Installation (pdf format)

Download from Repository

You can to download the binary tar.gz version from our Repository section in:

Software Repository

Remember: tccguest / guest1$

Current Versions

kimik.iciq.es: Jmol-9

p021: Jmol-11.2.23

Supported Molecular File Formats

   * ADF output - SCM.com [1]
   * CIF/mmCIF  - Crystallographic Information File and Macromolecular Crystallographic Information File, the standards from the International Union of Crystallography
   * CML - Chemical Markup Language
   * CSF - Fujitsu CAChe chemical structure, now Fujitsu Sygress
   * CTFile - Elsevier MDL chemical table
   * GAMESS - General Atomic and Molecular Electronic Structure System output, Gordon Research Group, Iowa State University
   * Gaussian 94/98/03 output - Gaussian, Inc.[2]
   * Ghemical
   * HIN - HyperChem from Hypercube, Inc.
   * Jaguar - Schrodinger, LLC
   * MM1GP - Ghemical molecular mechanics
   * MOL - Elsevier MDL structure
   * MOLPRO - Molpro output
   * MOPAC - MOPAC 93/97/2002 output (public domain)
     - MOPAC 2007 (v.7.101) graphf output (.mgf files) (public domain) [starting Jmol 11.1.28; reads coordinates, charges, and molecular orbitals]
   * NWCHEM - NWChem output, Pacific Northwest National Laboratory
   * odydata - Odyssey data, WaveFunction, Inc.
   * PDB - Protein Data Bank, Research Collaboratory for Structural Bioinformatics
   * QOUT - Q-Chem, Inc.
   * SDF - Elsevier MDL structure
   * SHELX - Structural Chemistry Department, University of Göttingen (Germany)
   * SMOL - Spartan data, Wavefunction, Inc.
   * xodydata - Odyssey XML data, WaveFunction, Inc.
   * XYZ - Minnesota Supercomputer Institute XMol file
   * XYZ+vib - XYZ format files with added vibrational vector information
   * XYZ-FAH - Folding@home XYZ file

Useful Links

Jmol website: [3]

Povray website: [4]