Support/Windows

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 on Windows

Jmol runs without problems on Windows 9x/XP machines using Sun's java virtual machines, both as Applet as well as 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 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"

• Start in: you can put your working folder, if you want; that will be the default location Jmol will show on "File > Open".

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

Associating molecular files (e.g. PDB) in hard disk with Jmol application

You can configure Windows Explorer (file manager) so that double-clicking on a pdb 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, Jmol.jar (you decided where to put it when you uncompressed the downloaded Jmol distribution file, jmol-10.xx.xx-binary.tar.gz or jmol-10.xx.xx-binary.zip).
2. Locate the file javaw.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 "Tools → Folder options", "File types" tab, and scroll to PDB (or any other extension that you want associated to Jmol, like MOL 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"

Contributors

AngelHerraez, NicolasVervelle, Pimpim