From Proteopedia

Jump to: navigation, search

Pages in Proteopedia use a javascript form of Jmol called JSmol, which operates automatically within a web browser. No installation or setup is needed. For some advanced projects, you may wish to use the Jmol standalone application (no web browser involved once it is downloaded). Here are instructions:

  • The Jmol application requires Java (free) in order to run. You can download and install it easily at
  • 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 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", 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).

Loading a 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" in the white window (without typing the quotation marks). The "=" tells Jmol to get the file from the Protein Data Bank. Substitute your PDB code for 1d66.
    • 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.

Commands and Script Files

You are now ready to enter Jmol commands into the Jmol Script Console. It is usually convenient to gather commands in script files. Command script files must be edited with a plain text editor. The names of command script files should always end .spt. You can run a script file by dragging it and dropping it into the molecular graphics window of Jmol.

See Also

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

Personal tools