by: sean cain
DESCRIPTION
Rendering Differences Between Three-Dimensional Geometric Objects and Two-Dimensional Geometric Objects Using a DNA Rendering Program Written with the OpenGL Graphics Library. By: Sean Cain. Goals. Create a program able to render B-DNA in three dimensions accurately - PowerPoint PPT PresentationTRANSCRIPT
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Rendering Differences Between Three-Dimensional Geometric Objects
and Two-Dimensional GeometricObjects Using a DNA Rendering
Program Written with the OpenGL Graphics Library
By: Sean Cain
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Goals Create a program able to render B-DNA in
three dimensions accurately
Determine differences between rendering three-dimensional and two-dimensional geometric objects (lines vs cylinders)
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Background DNA
Forms a double helical structure Purines: Adenine (A) and Guanine (G) Pyrimidines: Cytosine (C) and Thymine (T)
Base-pairs Adenine only pairs with Thymine Guanine only pairs with Cytosine Adjacent pairs connected with a sugar
phosphate backbone
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Parameters
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DNA Rendering Program Tool to render B-DNA in three dimensions
Written in C# with OpenGL graphics library Input
DNA base abbreviations (A, C, G, or T) Output
A double helical strand of DNA based on input
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Program Issues Different sources for backbone and bases
The coordinates don't match up Bases
Plotted according to the coordinates in [4] Not all base-pair parameters, step
parameters, or local helical parameters were taken into account outside of the provided coordinates
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Issues cont. Backbone
Plotted according to the coordinates in [5] Translations were performed to line up the
backbone with the bases Rotations were not performed
A source with proper angles between adjacent backbones could not be found
Hydrogen atoms not rendered No exact coordinates Bond distance was the only measurement
obtained
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Issues cont.
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Two-dimensional Geometric Objects
Lines – bonds between atomsglBegin(GL_LINES);glVertex(x, y, z);glVertex(x, y, z);glEnd();
No extra operations are required to get proper placement and alignment of lines
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Three-dimensional Geometric Objects
Require a quadric object in OpenGL Quadric objects are defined in [5] by the
following quadratic equationa1x
2 + a2y2 + a3z
2 + a4xy + a5yz + a6zx + a7x + a8y + a9z + a10 = 0
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Three-dimensional Geometric Objects cont.
Cylinder – bonds between atomsgluCylinder( quadric, base, top, height, slices, stacks);
Cylinders aren't drawn with endpoints as lines are
A function renderCylinder() needed to be created to obtain proper alignment of each cylinder
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Three-dimensional Geometric Objects cont.
Sphere – atomsgluSphere(quadric, radius, slices, stacks);
Drawn at the origin Translations required to get proper placement
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Experimental Setup DNA Rendering Program was modified
Added a timer Strands were input before execution to avoid
user delay Strands were rendered with lines or cylinders
and with or without spheres Each strand was rotated 360° around the z-axis
49 different times The program rotated the strand 1° for every
call of the OnPaint() function independently with no user input
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Results Average timing differences between lines
and cylinders with and without spheres are represented in the following graphs
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Future Work Properly align sugar phosphate backbones Include base-pair, step, and local helical
parameters Include different ways for user to input data
Mouse translations and rotations Collect more data with different operations
– Translations
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Bibliography1.) Neon Helium Productions". May 06 2010 <http://nehe.gamedev.net/>
2.) CodeGuru". May 06 2010
<http://www.codeguru.com/forum/archive/index.php/t-228231.html>
3.) Olson, Wilma et. al.. "A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry". Journal of Molecular Biology 2001: 229-237
4.) Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A.T. and Berman H. M. "New parameters for the refinement of nucleic acid-containing structures". Acta. Cryst. D52 1996: 57-64
5.) May 06 2010 <http://www.movesinstitute.org/~mcdowell/mv4202/notes/lect11.pdf>
6.) May 06 2010 <http://www.chemicalgraphics.com/paul/images/DNA/BallAndStick.jpg>
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Questions?