Athena Molecular viewer (supports
Technologies employed: [Linux/Solaris versions]
from the larger Zeus
Molecular visualisation project
Translate and Zoom into the molecular model
atoms and bonds within molecules.
molecular model residue sequence
Atom and Bond Lists
various industry & academic standard file formats
Download a PDB from RSCB server
User can also customize the request URL
derived from the larger Zeus
project and is an experimental molecular visualisation project. Athena uses the
Sun (now Oracle) Java-3d
visualisation library that wraps OpenGL/DirectX. Designed to run on the
Solaris Unix operating system Athena also runs on Windows via the Java Virtual
Unlike Zeus which employs the LWJGL
(Light-weight Java Gaming Library), Athena makes use of the Java-3d
rendering libraries. 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 to render.
– uses Van der waal’s Radii to size atoms appropriately
Bezier “Bernstein” function through peptide/nucleic acid backbone
ribbon, line or tube rendering
invididual Atom colours
residue/nucleic acid colour
acid type colours
Colouring of residues (CPK, by type
Download and install Athena
Athena for Oracle/Sun Solaris Unix (Sparc-32)
Zip of Jar built for Oracle/Sun Solaris 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
- Run athena directly:
java -Djava.library.path=. -jar ./Athena-sparc-32.jar
for Microsoft Windows (x86)
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)
Zip of Jar built for Linux 32-Bit (~4.5mb) ]
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.
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.