1. Visualizing Molecules Shuchismita Dutta September 2008

2. Visualization Overview Visualization Why visualize? Data How to visualize? –Introduction to RasMol –Introduction to Chimera

3. Visual storytelling http://dd.dynamicdiagrams.com/?p=541 Road sign near Niagara Falls. Picture posted by Tim Roy

4. Why Visualize? Summarize information (data) –what, where, how many? –mechanisms –change –cause and effect Communication and decision making aid Human eye is very effective in pattern recognition

5. Data What, where, how many? –Quantitative vs Qualitative –Discrete vs Continuous Change –Detail –Comparison Mechanisms –Cause and Effect –Intermediate steps

6. What, where, how many? Phe, Arg Chains in rainbow coloring

7. Change and Mechanism

8. How to visualize? http://www.umass.edu/microbio/rasmol/history.htm

9. Visualization - Physical Models Wire models (1958) Richard’s box (1958) Ball and Spoke (1960) Byron’s bender (1970s) Rapid prototyping (1990s) Toobers (2000s) www.umass.edu/microbio/rasmol/history.htm Byron’s bender Rapid prototyping Laser crystal Toobers

10. Visualization – Computer Models Early computers (1960s-70s) TAMS (1980s) Evans & Sutherland (1980s-90s) Modern computers (1990s …) Kinemage, Rasmol, Chimera … Ribbons Wireframe Ball and StickSpace fillSurface

11. What is this? Blood – By David Goodsell 2000 Hemoglobin Low density lipoprotein Immunoglobulin Cell membrane Spectrin Complement C1 Fibrinogen Albumin

12. Roger Hayward Linus Pauling Irving Geis Richard Dickerson Drawing Molecules

13. Visualization Software Needs Rotate and translate molecule(s) Color specific parts of the molecule Label residues and atoms Geometrical measurements (distances & angles) Schematic representation: –Atoms/Bonds/Secondary structures, … –Molecular surfaces –Volumes Compare structures Save pictures

14. Visualization Metaphors Spacefill WireframeRibbons What does a molecule look like?

15. Style and Purpose Overall shape & structure – space fill Fold, classification etc. - ribbons Biologically significant regions - ball & stick, stick –Understand binding geometry –Design activators, inhibitors, drugs Because molecules are complex and beautiful – mixed or other creative representations

16. Visualize molecules on a computer 1. Coordinate file from PDB 2. Visualization software RasMol, Chimera, Swiss PDB Viewer etc. 3. Computer 4. Molecule image

17. The PDB format file Where to find it? What does it contain? What is visualized?

20. Examples 2bwh (myoglobin, X-ray) 1nau (glucagon antagonist, NMR)

21. Which program should I use? All modeling programs have many basic features in common Once you learn to use one molecular modeling program, it's much easier to learn the next one Try different programs and select the best one for you Knowing well one or two programs is enough

22. Learning to use RasMol, Chimera Display Color Select H-bonds Measure distances Make assemblies RasMol demonstration using 1ZAA Chimera demonstration using 1AEW; Hands on exercises on Hemoglobin (4hhb, 1hbs) and Myoglobin (2mm1)

23. Sickle cell anemia learn.genetics.utah.edu/.../sicklecell/index.cfm Journal of Molecular Recognition, Volume 17, Issue 5 (p 497-504) 1 2 3

24. Making Depositions Introduction to Drupal