Molecular and MotifSpace Visualization Toolkit : RasCtrl

1. Molecular and MotifSpace Visualization Toolkit : RasCtrl Jingdan Zhang

2. 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. 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. 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. Our Goal • Develop a toolkit to visualize queried motifs • Show spatial configurations • Show position/structure correlations

6. 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. 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. 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. Solution Architecture Demo Architecture

10. 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. Two Stages of Development II • Stage Two: add functions to support motif visualization • Motif structure alignment between proteins Demo

12. Demo • Build a molecular visualization application in one minute.