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