1. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Molecular and MotifSpace Visualization Toolkit : RasCtrl Jingdan Zhang

2. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Molecular Visualization Molecular visualization ♦ Display a 3D model of a molecule to illustrate its physical form and structure. Rich representation models ♦ Lines and sticks ♦ Spheres ♦ Ribbons and cartoons ♦ …

3. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Molecular Visualization Molecular Visualization is a hot research area ♦ More than 50 years of history ♦ Experienced rapid development in recent years Progress in the bio-informatics research Progress in graphics techniques Wide applications ♦ Drug design ♦ Protein structure analysis ♦ Education

4. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Molecular Visualization Packages Many visualization packages ♦ Commercial ♦ Open source Rasmol –Originally developed by Roger Sayle at 1993, continually evolved over the last ten years –The code is well written and compact –Several widely used programs are derived from Rasmol: Rastop, Chime, Programs for education purpose VMD –Developed by UIUC since 1995 –Visualize Molecular Dynamics –A large set of functions to support wide applications Pymol –Python-enhanced molecular graphics program

5. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Our Goal Develop a toolkit to visualize queried motifs ♦ Show spatial configurations ♦ Show position/structure correlations

6. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Design Issues Support common molecular representations ♦ Lines and sticks ♦ Spheres ♦ Ribbons and cartoons Support Microsoft Smart Client architecture ♦ Currently, no major open source visualization tools support smart Client architecture Flexible and easy to use ♦ Can plug into applications easily ♦ Support drag & drop interface design

7. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Design Strategy Use Microsoft ActiveX technique to build the toolkit ♦ To create a re-usable molecular visualization component ♦ Can be converted to the windows Forms control by.Net framework tool Aximp.exe Develop the toolkit based on the open source program Rasmol ♦ Rasmol supports a variety of standard molecular representations ♦ The original code is well written and compact, only 20k lines of code

8. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Functionality of RasCtrl Parse PDB files to build protein data structures Render proteins using a variety of representation Support MotifSpace visualization Respond to user interaction

9. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Solution Architecture Architecture Demo

10. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Two Stages of Development I Stage One: modify original Rasmol code to create an ActiveX component From C code to C++: get rid of static and global variable to enable multiple instances of RasCtrl running at same time. Use interface functions to wrap original functions RasCtrl Interface CRasAdapter CRasmol

11. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Two Stages of Development II Stage Two: add functions to support motif visualization ♦ Motif structure alignment between proteins Demo

12. The UNIVERSITY of NORTH CAROLINA at CHAPEL HILL Demo Build a molecular visualization application in one minute.