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Jmol

  1. Jmol
    1. Description
    2. Version
    3. Authorized Users
    4. Platforms
    5. Local Documentation
      1. Modules
      2. Execution
    6. Documentation

Last Modified: 06/26 11:08

Description

Jmol is an open-source Java viewer for chemical structures in 3D.

Version

  • 11.6.24

Authorized Users

  • circe account holders

Platforms

  • circe

Local Documentation

Modules

Jmol requires the following module file and a prerequisite to run:

  • apps/jmol/11.6.24

To run Jmol on the cluster, ensure that you use module initadd to make the changes persistent. See Modules for more information.

Execution

First, you will need a protein or molecule to play with. Go to  http://www.rcsb.org/pdb/ and grab one in .pdb format. Other supported filetypes are listed here:  http://jmol.sourceforge.net/#What%20Jmol%20can%20do

Next, start jmol: 

$ jmol

Finally, go to File->Open and open your molecule file.

Documentation

You'll need to have XWin32 set up correctly to run Jmol. See our XWin32 documentation for more details: XWin32

Detailed documentation on using JMol can be found here:  http://wiki.jmol.org:81/index.php/Main_Page