Support/Osx

Jmol + JSmol Documentation

• Description of files in Jmol+JSmol distribution
• File formats read or written by Jmol
• The Jmol scripting interface
  • Scripting as a programming language
  • Complete reference of scripting commands:
    • at St Olaf (primary site)
    • at Jena3D (mirror)
• Loading models directly from databases
• Mouse manual
• Default colors used by Jmol
• Atom sets predefined in Jmol
• Support for bond orders · isotopes · stereochemistry · hydrogen bonds
• Jmol as editor
• Multi-touch support
• Copying and pasting state scripts between applets.
• Backward compatibility (changes of behavior across versions)
• Features added since version 10
• Users mailing list (and a mirror)

Jmol application

Jmol is fully compatible with MacOS X with Java installed.

• Problem: macOS blocks execution of Jmol.jar (in recent versions of macOS and Java, 2024)
  • When you double-click on the Jmol.jar file, a warning says something like this:

"Jmol.jar" cannot be opened because it is from an unidentified developer. macOS cannot verify that this app is free from malware.

• Solution: right-click or Ctrl-click on the file, a menu will open, choose "Open" (or "Open with Jar Launcher"), accept the warning giving the permission and choose "Open" again. After the first time, you will probably be able to just use double-click.

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 Jmol.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 Jmol.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 http://waterontheweb.org/data/java/trouble.html 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 http://sourceforge.net/projects/javaplugin/ and click the Download link. Choose JavaEmbeddingPlugin0.8.7.zip, 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: JavaEmbeddingPlugin.bundle and MRJPlugin.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

OS	Mac OS X
Java vendor	Apple Computer, Inc.
Java version	1.4.2_05

• you can test Jmol here http://jmol.sourceforge.net/demo/.

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:

• Mac OS X 10.5 "Leopard"
• Mac OS X 10.4 "Tiger"

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

Contributors

AngelHerraez, Corriecas, Hansonr, NicolasVervelle, Pimpim