Jamie J. Alnasir

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

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Zeus molecular visualisation software

Technologies employed: [Win ver.] Delphi Pascal/OpenGL [Linux ver.] Java/OpenGL

Zeus Molecular visualisation software for Windows

In the making: Java edition (Zeus-Java) for Linux, Mac 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 (~1mb) - recommended]

Java version of Zeus

Provided below are downloads of Zeus-Java edition (require Java runtime but do not need installation on the client workstation). Zeus-Java is an alpha version and hence might be "buggy" and may not have all the features implemented in the Windows version above.

[ Download JAR built for Windows 32/64-Bit ]
[ Download JAR built for Linux-32-Bit ]
[ 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.

A future aim is to produce a single multi-platform JAR for Zeus-Java which will run on all of the above platforms.

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