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

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)

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

Parameters

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

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

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

Issues cont.

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

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

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

Three-dimensional Geometric Objects cont.

Sphere – atomsgluSphere(quadric, radius, slices, stacks);

Drawn at the origin Translations required to get proper placement

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

Results Average timing differences between lines

and cylinders with and without spheres are represented in the following graphs

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

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>

Questions?