Jmol

Jmol

Description

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

Version

  • 11.6.24

Authorized Users

  • CIRCE account holders

Platforms

  • CIRCE

Running Jmol on CIRCE

Modules

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

  • apps/jmol/11.6.24

See Modules for more information.

Starting the Application

Before you login to CIRCE, you need to make sure you have X11 Forwarding enabled. If you’re logging in from a UNIX/Linux system, you will need to do the following:

ssh -Y user@circe.rc.usf.edu

Then, 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:

Simply type jmol at the command prompt AFTER loading the proper module (see above) in your terminal window. If you have properly configured an X11 session, you should see the full Jmol interface.

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

For Windows, Mac, and Linux users, Jmol can also be launched through the CIRCE Desktop Environment using a terminal. For more information about the CIRCE Desktop Environment, please see our CIRCE Desktop Environment documentation.

Documentation

Reporting Bugs

Report bugs with Jmol to the IT Help Desk: rc-help@usf.edu