Jmol/Application

Pages in Proteopedia use the applet form of Jmol, which operates within a web browser. For some purposes, you may wish to use the Jmol application. Here are instructions:

• Put Jmol.jar in your working folder: Create a folder (directory) on your computer in which to work. Go to Jmol.Org, select Download (upper right), go to the Jmol Downloads Page, and download the current version as a binary.zip file. Double click the zip file to unzip it, and copy the file Jmol.jar (one of a large number of files in the zipped download). This is the Jmol application. Paste it into your working folder.

• Run the Jmol application: Double-click Jmol.jar in your working folder, and a black window will appear titled "Jmol".
  • Important for macOS: The first time you run Jmol.jar, right click on it and select "Open with Jar Launcher.app", and then give permission. After doing this once, you can simply double-click on Jmol.jar to run it.

• Open the Jmol Script Console: If the white "Jmol Script Console" window does not appear, use Jmol's File menu (at the top), Console to open it. Now you are ready to enter commands (see the Jmol Interactive Scripting Manual).

• Load your molecule. There are several ways to load a PDB file:
  • If you do not have a downloaded copy of the PDB file:
    • Enter the command "load =1d66". The "=" tells Jmol to get the file from the Protein Data Bank.
  • If you have downloaded the PDB file:
    • Drag the file and drop it into the black Jmol window.
    • Enter the command "load ?", and a file picking dialog will appear.
    • Open Jmol's File menu (above the black window), and Open or Open Recent.

See AlsoSee Also

• Jmol
• Pages about Jmol-specific topics