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Athena Molecular Viewer

Athena is an experimental molecular visualisation project  derived from the larger Zeus project. Athena uses the Sun (now Oracle)  Java-3d visualisation library that wraps OpenGL/DirectX. It is designed to run on the Solaris Unix operating system but also runs on Windows via the Java Virtual Machine.

(Above) Sun Blade 1500 (Red) workstation featuring the  UltraSPARC IIIi 64-bit processor
The use of the Java-3d rendering libraries within Athena differs significantly from the use of LWJGL (Light-weight Java Gaming Library) in Zeus. The LWJGL is an OpenGL wrapper that simply exposes OpenGL functions to Java whereas Java-3d uses an object orientated means of  constructing directed acyclic graphs to generate the rendering scene which it then uses OpenGL/DirectX native libraries to render.

The purpose of adapting and re-writing the core rendering engine of Zeus was in order to construct molecular visualisation models using directed acyclic graphs and also to support the
Solaris Unix platform and UltraSPARC IIIi processor.

Athena running on Solaris (Sparc) on a Sun Blade 1500

(Above) Athena running on a Sun Blade 1500 (Red) workstation

Download and install Athena

Athena for Oracle/Sun Solaris Unix (Sparc-32) 

[ Download Zip of Jar built for Oracle/Sun Solaris (sparc) 32-Bit (~4.4mb) ]

1. Unzip contents of Zip file into the /usr/athena/ folder (which will need to be created)
2. To run

  • Copy a link to the the run-athena.sh script to your Desktop or run from
    OR
  • Run athena directly:
    cd /usr/athena
    java -Djava.library.path=. -jar ./Athena-sparc-32.jar



Athena for Oracle/Sun Solaris Unix (Solaris on x86 (32-bit)) 

[ Download Zip of Jar built for Oracle/Sun Solaris (x86) 32-Bit (~4.4mb) ]

Install (as above), but this version is built for Sun/Oracle Solaris running on (x86 CPUs)


Athena for Microsoft Windows (x86)


[ Download Zip of Jar built for Microsoft Windows 32-Bit (~7mb) ]

1. Athena windows is provided as a self-contained EXE installer program
2. A 32-bit JVM (Java Virtual Machine) must be available (or a 64-bit JVM supporting 32-bit) via the path.
3. Java-3d libraries are provided with the installer, should you wish to install them manually they are freely available from Oracle's Java3d website (ensure the correct version is downloaded).

Athena for Linux (x86)

[ Download Zip of Jar built for Linux 32-Bit (~4.5mb) ]
[ Download Zip of Jar built for Linux 64-Bit (~4.2mb) ]


1. Athena Linux is provided as a self-contained JAR
2. For the 32-bit version a 32-bit JVM (Java Virtual Machine) must be available (or a 64-bit JVM supporting 32-bit) via the path.

NB: Linux version requires setting the "executable bit". Once downloaded right-click and navigate to "properties->permissions." Turn "executable" bit on. and open with Java runtime environment.