Overview
Drawing Carbohydrate
Cartoons
I. Eborn and A. Burger
Supervised by Dr M. Kuttel and Dr J. Gain
The Problem
The problem: visualising molecules
The move to carbohydrates
The project
Additional visualisation techniques
Design/development approach
Evaluation methods
Division of labour
Optional extras
Ribbon view of protein using VMD
Conventional molecular views can be
cluttered
Makes it difficult to discern overall structure
Want a clear representation of molecule’
molecule’s
structure, not necessarily a “realistic”
realistic”
image
Ribbon techniques for proteins and DNA
were developed almost 20 years ago
The move to carbohydrates
Ribbon views of proteins have proven
useful to researchers
Knowledge of structure can help to predict
function
No current equivalent for visualising
carbohydrate structure
The benefits would be similar
Algorithm needs to give good results for
connected ring structures, not just chains of
atoms
Traces “backbone”
backbone” consisting of certain atoms
within the molecule
The project
Develop an algorithm for visualising
carbohydrates
Analyse molecule data and generate
geometry
Emphasis on revealing structure
Implement a molecular viewer that uses it
Implement additional visualisation
techniques
1
High-level view of the system
NonNon-photorealistic lighting model
File loader
Intermediate
structure
Conventional
molecular view
Carbohydrate
algorithm
Geometry
Lighting model
Ian
Depth cues
Visualisation techniques
Preserves detail in shadowed areas
Silhouettes
Emphasise individual scene elements
Depth cues
Silhouettes
Fog, texture, shadows (ground plane)
GUI/Renderer
Anton
Design/development approach
Design
Evaluation methods
User testing
Collaborative design of module interfaces
Individual design of internals
Development
ParedPared-down Extreme Programming approach
Emphasis on testing
Reduced emphasis on iteration
Initial development of prototype interface
Serves as testing platform for other modules
Followed by development of everything else (in order
of precedence)
Division of labour
Joint development of carbohydrate algorithm
Ian:
GUI using FOX windowing toolkit
Lighting model
Depth cues
Anton:
Carbohydrate algorithm implementation
File format support
Silhouettes
To determine utility of carbohydrate
visualisation algorithm
To measure effectiveness of other
visualisation techniques in molecular viewing
context
Test subjects from chemistry department
Academics if possible, students otherwise
Optional extras (if time)
Movie output
Using a predefined sequence of frames
Distortion viewing
Pushes surrounding geometry away to emphasise
and clarify focal point
Viewpoint selection
Automatic selection of viewpoint for emphasis on
structure and/or connectivity
2D “flattened”
flattened” view
Using graph layout techniques for aesthetically
acceptable results
2
Questions?
3
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