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Jmol

Introduction

Jmol is a simple molecular visualization program. It can read various file formats and can write various formats. Animations of normal modes and simulations are implemented. Jmol is an OpenScience Java application. The plan is to provide enhanced XMol functionality. The Jmol Home Page .

Version

Versions 0.6.1 and 10.2.0 are available at OSC.

Availability

Jmol is available on the Pentium 4 Cluster. Version 0.6.1 is quite old and may not work with some
recent output files, but it responds quickly. Jmol is best executed locally. Thus, we recommend downloading the latest version from http://jmol.sourceforge.net/download/. The installation process is trivial.

Usage

Open Science Project. No license agreement.

Jmol Usage on the Cluster at OSC

Location

The root of the Jmol directory tree is /usr/local/jmol

Execution

For convenience aliasing is recommended:

Shell	Command
csh	alias jmol /usr/local/jmol
ksh	alias jmol=/usr/local/jmol

Examples

Example data files are in the samples subdirectory.

Documentation

General documentation is not yet available from the Jmol Home page nor in the local machine directories. See the Usage section for the location of the root of the Jmol directory tree on each machine and for machine specific documentation.