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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.
  • This is probably no longer important: Free java memory if your project involves large molecules or assemblies. This is not necessary if your molecule(s) are modest in size (up to ~30,000 atoms). If you skip this step and Jmol gives you an "Out Of Memory" error, then come back and do this step. Close any java-based programs. Close all browser windows or tabs that contain the Jmol applet. Close the Jmol application. You can check Jmol's java memory usage by clicking on Jmol (in either the applet or the application), then on the main menu, About, System.
  • Run the Jmol application: Double-click Jmol.jar in your working folder, and a black window will appear titled "Jmol".
  • 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).
  • This no longer seems necessary for OS X: Copying and pasting: To copy or paste commands in the white Jmol Script Console window, use Ctrl-C and Ctrl-V, even if working on an Apple Mac OS X!. In java windows, the usual Apple Cmd-C and Cmd-V don't work! You can also select blocks of text with your mouse, then drag and drop them.

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

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