Jamie J. Alnasir


  Dr. Jamie J. Alnasir M.Pharm (Hons), PhD researcher, IT Consultant, Photographer, amateur tennis player...


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Zeus molecular visualisation software

Technologies employed: [Win ver.] Delphi Pascal/OpenGL [Linux ver.] Java/Java3D (Now JavaFX)




Zeus Molecular visualisation software for Windows

In the making: Athena for Linux and platforms running the Java Runtime Environment

Core features        

  • Rotate, Translate and Zoom into the molecular model
    • View by Residue chain type
    • View by residues by Chain
  • Calculate Hydrogen bonds
  • View atoms and bonds within molecules.
  • Residue labelling
  • Measure distances/angles

Supports various industry & academic standard file formats

  • Brookhaven PDB
  • Mol format
  • Mol2/SYBYL format
  • XYZ format

Remote Download a PDB from RSCB server
– User can also customize the request URL

Powerful Sequence Searching capabilities

  • Sequence Search/Highlight
    • Wildcard search capability
  • Residue/Base keypad
  • Display molecular model residue sequence

 

Export rendering as a bitmap

Exhaustive Atom and Bond Lists

Export rendering as a bitmap

Exhaustive Atom and Bond Lists

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  

Highlighting of residues

 Peptide structure “Ribbon”

  • 3d Bezier “Bernstein” function through peptide/nucleic acid backbone

  • Supports ribbon, line or tube rendering

 Control of rendering quality to allow user flexibility with performance/rendering quality  

Ramachandran plot of protein structure

  • Zeus can produce high quality Ramachandran plots of dihedral angles to easily elucidate secondary structure

  • Protein structure can be viewed through a list of calculated Psi, Phi and Omega dihedral angles for each of the amino acid residues in the sequence.

  • Plots can also be made on a user chosen/loaded bitmap image allowing a ramachandran graph to be plotted over a standard distribution.

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..)

Windows version of Zeus

[ Download and Install (~5mb) - recommended]


Athena (Basic Java version of Zeus)

Provided below are downloads of Athena molecular viewer (these require Java runtime but do not need installation on the client workstation). Athena is an alpha version and hence may not have all the features implemented in the Zeus for Windows version (above).

[ Download JAR built for Linux-64-Bit ]
[ Download JAR built for Macintosh OSX - coming soon! ]

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.


[ Download Installer EXE built for Windows 32/64-Bit ]


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