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 double-click Jmol.jar, macOS will refuse to run it. Open System Settings and go to Privacy & Security. Scroll down near the bottom, where you will see, under the Security section, "Jmol.jar" was blocked to protect your Mac. Click the button Open Anyway (twice). After doing this once, in future, 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).

• There are several ways to load a PDB file:
  • If you have downloaded the PDB file:
    • Drag the file and drop it into the black Jmol window.

See Also

• Jmol
• Pages about specific Jmol topics

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz