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This video demonstrates our impostering 
framework for accelerating the rendering

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of quadric elements such as spheres,
cylinders and helices

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for visualization of large bio-molecules

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We implement our framework in ProteinVis

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a tool for visualizing various
representations of large biomolecules

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using standard desktop graphics
hardware

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proteinvis has been developed at

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Visualization and graphics lab, 
Indian institute of science Bangalore.


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The space-fill model is a common representation 
of primary structure of molecules

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where atoms are represented as spheres

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with radii set to their van-der-waals radius

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In our framework we first render a rectangular imposter

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that covers the sphere's rasterization

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Each raster fragment is then checked 
to see if it belongs to the sphere

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If it does not, it is discarded.

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The retained fragments are depth corrected and colored

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using accurate surface normals

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This allows accurate rendering of spheres at any resolution

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Here we render the GroEL/1AON molecule

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which consists of approximately 60,000 atoms

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ProteinVis uses our framework for this purpose

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and achieves a framerate of about 55-60fps

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the details of the card are as shown

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The ball-stick model is another common 
representation of the primary structure of molecules

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where atoms are represented as uniformly sized spheres

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and bonds between them as cylinders

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similar to spherical imposter,

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The cylinders are first approximated by a bounding cuboid

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and the imposter's retained fragments

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are depth-corrected and colored with accurate normals

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The spheres are then rendered using 
the spherical imposter primitive.

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Proteins consist of a contiguous chain of
amino acids referred to as the backbone

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They are commonly represented by sampling 
line segments from a spline curve

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passing through the alpha carbon atoms

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of each of the amnio acids

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The cylinder imposter method demonstrated earlier

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is used for each line segment to produce a tube like object

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The imposter is modified so that there 
are no gaps between continuous segments

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Surface normals are interpolated
consistently across consecutive

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cylindrical segments to ensure smooth shading.

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Oftentimes, weak hydrogen bonds form across 
amino acids in the backbone chain of proteins

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leading to the formation of secondary
structures such as alpha-helices and beta-sheets

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The alpha helix commonly exhibits 
high structural regularity

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with the helix executing a turn for 
every 3.6 amino acids in the backbone

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and a pitch of 5.4 angstroms

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Also, the coiling is regular across a standard axis

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We levrage on this regularity,

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to fit a cylindrical imposter across this axis

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that is appropriately culled to reveal the helical structure.

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In conclusion, we have presented our framework

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to accelerate the renderings of large molecules

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by augmenting the OpenGL pipeline with
spherical, cylindrical and helical elements.

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We applied our method to accelerate various representations

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of primary and secondary protein structures

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such as the space fill, ball stick, 
backbone loop and alpha-helices.

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By using fewer primitives to represent the structure,

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we utilize lesser graphics memory and 
can scale our frame work to large biomolecules

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while maintaining high quality 
and interactive framerates

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we conclude the video by giving a quantitative 
comparision of pymol against proteinVis

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The specs of the molecule and the card are as listed.