Difference between revisions of "Jmol"

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= [[Jmol]] =
== Description ==
== Description ==



Revision as of 14:55, 1 July 2016

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 holders
  • RRA account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • RRA cluster
  • SC cluster

Modules

Jmol requires the following module file to run:

  • apps/jmol/11.6.24

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!

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

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

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

Reporting Bugs

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