Portfolio
Zeus Molecular Viewer and Visualisation software
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
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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
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Powerful
Sequence Searching capabilities
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- Sequence
Search/Highlight
- Wildcard
search capability
- Residue/Base
keypad
- Display
molecular model residue sequence
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Export
rendering
as a bitmap
Exhaustive
Atom and Bond Lists
Export
rendering
as a bitmap
Exhaustive
Atom and Bond Lists
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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
Highlighting of
residues
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Peptide
structure “Ribbon”
-
3d
Bezier “Bernstein” function through peptide/nucleic acid backbone
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Supports
ribbon, line or tube rendering
Control
of rendering quality
to allow user flexibility with performance/rendering quality
Ramachandran plot of
protein structure
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Zeus
can produce high quality Ramachandran plots of dihedral angles to
easily elucidate secondary structure
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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.
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Plots
can also be made on a user chosen/loaded bitmap image allowing a
ramachandran graph to be plotted over a standard distribution.
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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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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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