CREST Workshop, 2014: Using Surfaces to Depict Contacts and Interactions

1. CREST Workshop, 2014: Using Surfaces to Depict Contacts and Interactions Bob Hanson St. Olaf College, Northfield, MN http://www.stolaf.edu/people/hansonr Center for Biomolecular Modeling Milwaukee School of Engineering Milwaukee, WI 6/2/2014

2. Rendering in Jmol Many rendering options, including cartoons,

3. Rendering in Jmol Many rendering options, including cartoons, transparency,

4. Rendering in Jmol Many rendering options, including cartoons, transparency, fog-like shading

5. Rendering in Jmol Many rendering options, including cartoons, transparency, fog-like shading 3D Ramachandron plots and Ramachandran angles

6. Jmol Sources on the Web http://www.rcsb.org

7. Jmol Sources on the Web http://www.rcsb.org Load “” FILTER “biomolecule 1”

8. Jmol Sources on the Web http://www.rcsb.org contact {ligand} surface

9. Jmol Sources on the Web http://www.rcsb.org write PNGJ “?myfile.png”

10. Jmol Sources on the Web http://chemapps.stolaf.edu script "http://chemapps.stolaf.edu/jmol/jsmol/spt/ext/rcsb/gotoLigand.spt" gotoLigand "1eve" "e20"

11. Jmol Sources on the Web function gotoLigand(xxxx,ligandAtoms) { // load with hydrogens (13.3.9_2013_11_13c) if (!ligandAtoms) { return } if (xxxx) { load @{"="+xxxx} filter "addhydrogens" } else { isosurface delete; contact delete; } if (ligandAtoms.type == "string" && !ligandAtoms.find("[")) { ligandAtoms = "[" + ligandAtoms + "]" } select @ligandAtoms ligandAtoms = {selected}[1] ligandAtoms = {within(group, ligandAtoms)} // contact surface //isosurface select {ligandAtoms} only vdw //isosurface slab 60 fullylit contact ID "surf" {ligandAtoms} surface contact slab 60 fullylit … http://chemapps.stolaf.edu script "http://chemapps.stolaf.edu/jmol/jsmol/spt/ext/rcsb/gotoLigand.spt" gotoLigand "1eve" "e20"

12. Surfaces: Van der Waals load :morphine or load $morphine (PubChem) (NCI Resolver) isosurface VDW or isosurface select {xxx} only VDW

13. Surfaces: Van der Waals isosurface VDW translucent 0.3

14. Surfaces: Van der Waals isosurface VDW frontonly translucent 0.3

15. Surfaces: Van der Waals isosurface VDW map MEP frontonly translucent 0.3

16. Surfaces: Solvent-excluded isosurface select {protein} only solvent

17. Surfaces: Solvent-excluded -- most sophisticated surface -- requires some time -- can be CACHED for PNGJ isosurface select {protein} only solvent

18. Surfaces: Solvent-accessible isosurface select {protein} only SASURFACE

19. Observations: Numerical data can be mapped onto atoms and surfaces for visualization

20. Surfaces: Numerical data can be mapped onto surfaces for visualization load =1crn isosurface solvent map property temperature isosurface colorscheme "bwr"

21. Surfaces: Numerical data can be mapped onto surfaces for visualization, or used to change atom properties, such as displayed atom radius load =1crn color property temperature “bwr” {*}.radius = {*}.temperature.all.div(20)

22. Surfaces: Cavities and Pockets load =1eve isosurface select {protein} only cavity

23. Surfaces: Cavities and Pockets load =1eve isosurface select {protein} only pocket cavity

24. Surfaces: Cavities and Pockets load =1eve isosurface select {protein} only pocket cavity isosurface slab none slab within 7.5 {e20} select protein wireframe -0.2 center e20 zoom {e20} 0 background black set zshade set zshadepower 3

25. Clipped Isosurfaces Idea: There are many more ways to clip an isosurface than just “within some distance of a set of atoms.”

26. Example: Static Mapped Surface Backdrop Isosurface slab off slab 50

27. Example: Dynamically Clipped Surfaces

28. Contacts Using Jmol, we have been experimenting with different ways of creating and using surfaces.

29. Contact Mapping Idea: Map a Van der Waals surface with data representing proximity to another surface. Color data red to indicate overlap of Van der Waals surface. Color data blue to indicate atoms far from contact.

30. Contact Mapping contact {ligand} SURFACE

31. Contact Mapping contact {ligand} TRIM

32. Contact Mapping contact {ligand} TRIM

33. Contact Mapping contact {ligand} HBOND

34. Contact Mapping contact … CONNECT

35. Contact Mapping contact … CONNECT

36. Contact Mapping

37. Contact Mapping

38. Contact Mapping

39. Contact Mapping

40. Contact Mapping

41. Contact Mapping

42. Surfaces: Electron Density Mesh

43. Surfaces: Electron Density Mesh load =1eve; display e20; zoomto {e20} 0

44. Surfaces: Electron Density Mesh isosurface “=1eve”

45. Surfaces: Electron Density Mesh isosurface “=1eve” isosurface display within 2.5 {e20}

46. Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.

47. Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.

48. Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.

49. Dynamic Volume Data Rendering Idea: Show actual crystallographic electron density data, and allow for dynamic clipping based on sigma values.