From Jmol
Jump to navigation Jump to search
Jmol + JSmol Documentation

Jmol application

Jmol is fully compatible with MacOS X with Java installed.

Jmol in web pages

Jmol is also compatible with MacOS X as a Jmol-Java applet in a webpage, subject to the browser supporting a Java plugin. Note that the use of Java in the browser may need to be enabled in MacOS configuration.

Jmol is also compatible with MacOS X as JSmol (HTML5, no Java) in a webpage.

Supporting Live Connect in non-Safari browsers

"2007 Nov 20. (posted by Bob Hanson)"

Jmol under MacOS X.5 on a new MacBook worked fine with Mozilla straight out of the box -- no Live Connect problems.

"2004 Nov 24. (posted by Timothy Driscoll)"

(2005 Dec 20: See note about Flock browser below)

The File icon.gifJmol.js file included with Jmol 10pre19 denies access to browsers that lack certain aspects of HTML and Javascript. This includes Live Connect support which, unfortunately, is not available in OSX browsers other than Safari.

Mozilla browsers on OSX (including Firefox) use their own JVM - which does not support Live Connect. they need to use the Apple JVM instead, in order to have a functioning Live Connect and pass the browser check in File icon.gifJmol.js.

Fortunately, there is a way to tell non-Safari browsers to use the Apple JVM. I have tested it in Mozilla and Firefox, and it works (OSX 10.3.6). Here are the configuration details:

  • Launch Mozilla and visit to verify your Java version. This page contains a small applet that reports the JVM details. it will probably say something like version 1.3.1.
  • Go to and click the Download link. Choose File, and select a mirror site. When the package is finished downloading, unzip it and open the folder.
  • Open the Binaries folder therein to see two files: File icon.gifJavaEmbeddingPlugin.bundle and File icon.gifMRJPlugin.plugin.
  • Copy these two files to /Library/Internet Plugins.
  • Launch Mozilla again. It should now be using the Apple JVM. To verify, go back to the url in step 1. it should report something like this:
Your system properties
Java vendor Apple Computer, Inc.
Java version 1.4.2_05

A Mozilla Variant That Works

I started using the Flock browser a few weeks ago; it's derived from Firefox and has some interesting blogging and community-bookmark features that aren't germane here. But imagine my surprise when I happened to point my Mac Flock browser at our Jmol-enabled site and saw the molecules displaying properly! Some invisibly-updated Java bugfix? Nope, Firefox itself is still broken. But Flock 0.4.10 works, on OS 10.4.3.

How to Create a Mac OS X Installer

With some simple steps you can pack Jmol into a proper Mac OS X application with a native installer. See instructions here:

(You can skip steps 1-6 which are for creating a Java app; just use File icon.gifJmol.jar from the Jmol distribution)