Jamie J. Alnasir


  Jamie J. Alnasir MPharm(Hons), PhD candidate, IT Consultant, Photographer, amateur tennis player...


 Home > Portfolio > Athena Molecular viewer for Linux, Windows, Solaris
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


 

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  


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.

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  

 

 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..)

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 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.


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