Jmol
Description
From the Jmol website: Jmol is an open-source Java viewer for chemical structures in 3D, with features for chemicals, crystals, materials and biomolecules
Version
- 11.6.24
Authorized Users
CIRCE
account holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
Jmol requires the following module file to run:
apps/jmol/11.6.24
- See Modules for more information.
Running Jmol on CIRCE
The Jmol user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.
- Note on CIRCE: Make sure to run your jobs from your $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Starting the Application
Establishing a GUI connection to CIRCE/SC
To use Jmol, you will need to connect to CIRCE/SC with GUI redirection, either using:
- CIRCE/SC Desktop Environment
- SSH with X11 redirection
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
[user@localhost ~]$ ssh -X circe.rc.usf.edu
or[user@localhost ~]$ ssh -X sc.rc.usf.edu
- If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
Once connected to CIRCE, you can open Jmol using the steps below:
[user@login0 ~]$ module add apps/jmol/11.6.24 [user@login0 ~]$ jmol
Finally, go to File->Open and open your molecule file.
Documentation
Home Page, User Guides, and Manuals
- Jmol Home Page
- Jmol Documentation
Benchmarks, Known Tests, Examples, Tutorials, and Other Resources
- PDB Database
Reporting Bugs
Report bugs with Jmol to the IT Help Desk: rc-help@usf.edu