Difference between revisions of "Jmol"

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


Jmol is an open-source Java viewer for chemical structures in 3D.
''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 ==
 
*<code>CIRCE</code> account holders
 
== Platforms ==
 
*<code>CIRCE</code>
 
== Running Jmol on CIRCE ==
 
=== [[Modules]] ===
 
Jmol requires the following module file and a prerequisite to run:


*<code>apps/jmol/11.6.24</code>
{{AppStandardHeader|11.6.24|jmol}}


See [[Modules]] for more information.
{{AppRunningOnAll}}


=== Starting the Application ===
=== Starting the Application ===


Before you login to <code>CIRCE</code>, 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:
{{X11Connection}}


<pre style="white-space:pre-wrap; width:35%; border:1px solid lightgrey; background:#000000; color:white;">
Once connected to CIRCE/SC, you can open Jmol using the steps below:
ssh -Y user@circe.rc.usf.edu</pre>
Then, you will need a protein or molecule to play with. Go to http://www.rcsb.org/pdb/ and grab one in <code>.pdb</code> format. Other supported filetypes are listed here: http://jmol.sourceforge.net/#What%20Jmol%20can%20do


Next, start jmol:
<pre style="white-space:pre-wrap; width:40%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ module add apps/jmol/11.6.24
 
[user@login0 ~]$ jmol</pre>
Simply type <code> jmol </code> 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-&gt;Open''' and open your molecule file.
Finally, go to '''File-&gt;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|CIRCE Desktop Environment]] documentation.
{{Documentation}}
*Jmol Home Page
**http://jmol.sourceforge.net/
*Jmol Documentation
** http://wiki.jmol.org


=== Documentation ===
{{BKETOR}}
 
*PDB Database
*Jmol Documentation
**http://www.rcsb.org/pdb/
** [http://wiki.jmol.org http://wiki.jmol.org]


{{ReportingBugs}}
{{ReportingBugs}}

Latest revision as of 21:43, 20 February 2017

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/SC

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

Once connected to CIRCE/SC, 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