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Athena Molecular Viewe, Visualisation software for Sun (Sparc) Solaris Unix
Athena Molecular viewer (supports
Solaris)
Technologies employed: [Linux/Solaris versions]
Java/Sun Java3d
- Derived
from the larger Zeus
Molecular visualisation project
- Rotate,
Translate and Zoom into the molecular model
- Calculate
Hydrogen bonds
- View
atoms and bonds within molecules.
- Display
molecular model residue sequence
- Exhaustive
Atom and Bond Lists

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Supports
various industry & academic standard file formats
- Brookhaven
PDB
- Mol
format
- XYZ
format
Remote
Download a PDB from RSCB server
–
User can also customize the request URL
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Athena is
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
Machine.
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.
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Rendering modes
- Wireframe
- Ball
and Stick
- Ball
and Wire
- Cylinders
- Triangular
Tubes
- Square
Tubes
- Space-filling
– uses Van der waal’s Radii to size atoms appropriately
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Peptide
structure “Ribbon”
-
3d
Bezier “Bernstein” function through peptide/nucleic acid backbone
-
Supports
ribbon, line or tube rendering
Flexible colour
configuration
- Select
invididual Atom colours
- Background
colour/Gradient colours
- Highlight
residue/nucleic acid colour
- Residue/Nucleic
acid type colours
Colouring of residues (CPK, by type
etc..)
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Download and install Athena
Athena for Oracle/Sun Solaris Unix (Sparc-32)
[ Download
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
OR
- Run athena directly:
cd /usr/athena
java -Djava.library.path=. -jar ./Athena-sparc-32.jar

Athena
for Microsoft Windows (x86)
[ Download Installer EXE built for Microsoft Windows 32/64-Bit (~11.6mb) ]
1. Athena windows is provided as a self-contained EXE installer program
2. Creates two batch files and shortcuts to run 32 bit and 64-bit versions on the JVM.
3. A 32/64-bit JVM (Java Virtual Machine) must be available via the path.
4. 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
Jar built for Linux 64-Bit (~5mb) ]
[ Download
Jar built for Linux 32-Bit (~5mb) ]
1. Athena Linux is provided as a self-contained JAR
2. A 64-bit JVM (Java Virtual Machine) must be available 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.
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