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Jmol + JSmol Documentation

Jmol on Windows

Jmol runs without problems on computers with Windows 95 or later, using Oracle's Java virtual machines, as an Application. Running Applets inside a web page relies also on the Java virtual machine, but has been disabled in most web browsers. The substitue for web pages is the JSmol object which runs without problems and provides the same functionality as the Jmol application.

Creating shortcuts to Jmol application

The details of creating a Windows shortcut and a Start menu entry are out of the scope of this wiki. What is given here are the specific details for Jmol.

Shortcut properties must be (under the Shortcut tab):

  • Target: the place where you have put Jmol files (usually when you uncompressed the distribution gz or zip file), including full pathname and filename and all between double quotes. Example:
"C:\Program files\Jmol\Jmol.jar"
For more flexibility, you may instead wish to call Java explicitly using this:
java -jar "C:\Program files\Jmol\Jmol.jar"
and if the system is not configured to locate the Java executable, you will need to indicate its full path, like e.g.
"C:\Program files\Java\jre1.8.0_251\bin\java" -jar "C:\Program files\Jmol\Jmol.jar"
These last two syntaxes allow to add extra start-up specifications, between java and -jar, like the amount of memory to be used, the window size, or the execution of a script, etc. (see Command line options).
For example, to force the Jmol interface in a language different from the system's language, you may add either of these to the target textbox (example for Brazilian Portuguese):
"C:\Program files\Jmol\Jmol.jar" -J "set language pt_BR"
java -Duser.language=pt_BR -jar "C:\Program files\Jmol\Jmol.jar"
Another example: to start Jmol running an initial custom script (set of commands), prepare such script in a text file and use this:
"C:\Program files\Jmol\Jmol.jar" -s "myScript.txt"
  • Start in: you can put your working folder, if you want; that will be the default location Jmol will show on "File > Open". If not specified, Jmol will ususally point to My documents, or Documents, or the Desktop.
  • Change Icon: you can get a Jmol icon from the Recycling Corner.

The same applies to entries in Windows Start menu, or Programs menu.

Associating molecular files in hard disk with Jmol application

You can configure Windows Explorer (file manager) so that double-clicking on a pdb file, or mol, xyz, etc. file (or right-clicking for options in the pop-up menu) will open it with Jmol application.

This is how to do it:

  1. Locate the application file, File icon.gifJmol.jar (you decided where to put it when you uncompressed the downloaded Jmol distribution file, File icon.gifjmol-11.xx.xx-binary.tar.gz or File
  2. Locate the file File icon.gifjavaw.exe in the Java installation folder (usually it will be somewhere like C:\Program files\Java\bin\).
  3. Open windows explorer / file manager, open menu "ToolsFolder options", "File types" tab, and scroll to pdb (or any other extension that you want associated to Jmol, like mol, mol2 or xyz). Select its entry.
  4. Click on "Advanced options" button and then either "Edit" the default "open" action or create a "New" action.
  5. In the textbox under "Action" you can type "open" or whatever you want it to be called in the pop-up menu; under "Application used" type (including the quotes and the final %1):
    "put here the path and filename of javaw.exe" -jar "put here the path and filename of Jmol.jar" "%1"
    For example:
"C:\Program files\Java\bin\javaw.exe" -jar "C:\Program files\Jmol\Jmol.jar" "%1"

Linking from PowerPoint to molecule files so that they open in Jmol application

You can set a hyperlink for any object in MS-PowerPoint that points to a pdb, mol, etc. file and have it opened in Jmol, by setting the default ("open") action of such file extensions, as described in the above sub-section.