Jmol/JSmol visualization

One of the simplest ways to visualize MOPAC outputs is by using Jmol and JSmol because MOPAC provides native support for these visualization tools. For information on obtaining and installing Jmol and JSmol, see the Jmol/JSmol website.

Jmol #

A Jmol-compatible MOPAC output file with the .mgf file extension is produced by adding the GRAPHF keyword to an input file. The .mgf output file can be opened in Jmol, which displays a ball-and-stick model of the output molecular structure. Molecular orbital isosurfaces can be viewed by pressing the right mouse button inside the Jmol viewer to open up a menu and then navigating through the “Surfaces” and “Molecular Orbitals” menu options for a list of MOPAC molecular orbitals to display as isosurfaces.

JSmol #

A JSmol-compatible MOPAC output file with the .html file extension is produced by adding the HTML keyword to an input file. For security reasons, modern web browser security prevents the use of local Javascript programs in HTML files. To use a local copy of JSmol with a MOPAC-generated HTML file, you should activate a local server from an active directory containing a JSmol installation in the /jsmol subdirectory. The HTML files should be located in this active directory or a subdirectory.

There are many ways to activate a local server. For example, a Python 3 installation can be used to activate a local server with the command:

python -m http.server

This activates a local server on port 8000, which can be viewed in a web browser at the URL http://localhost:8000. Other software might use a different port by default, and there are usually options to select the port used by the local server. The file structure of the local server is relative to the activate directory it was activated in. For example, if an HTML file molecule.html is in the active directory, then it can be viewed at http://localhost:8000/molecule.html. If the file is in a /mopac_data subdirectory of the active directory, then it can be viewed at http://localhost:8000/mopac_data/molecule.html.

When viewed from a web browser, the standard behavior of MOPAC’s .html output files is to display the output molecule in an interactive JSmol window. If separate MOPAC calculations were performed using the HTML and GRAPHF keywords, then the resulting .mgf file can be dragged and dropped into the JSmol window to enable viewing of the molecular orbitals. If a MOPAC calculation is performed with both the HTML and GRAPHF keywords, then the HTML file automatically loads the .mgf molecular orbital data into the JSmol viewer. JSmol has the same menu structure as Jmol for displaying the molecular orbitals as isosurfaces.

JSmol example #

As an example, a MOPAC calculation of benzene with Jmol and JSmol output enabled:

1SCF GRAPHF HTML
benzene

C  0.0000  1.3970 0
C  1.2098  0.6985 0
C  1.2098 -0.6985 0
C  0.0000 -1.3970 0
C -1.2098 -0.6985 0
C -1.2098  0.6985 0
H  0.0000  2.4810 0
H  2.1486  1.2405 0
H  2.1486 -1.2405 0
H  0.0000 -2.4810 0
H -2.1486 -1.2405 0
H -2.1486  1.2405 0

should produce an .html file that looks like this when viewed from a local server with JSmol located in the /jsmol subdirectory of its root directory.