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

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. Rendering in Jmol.

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

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  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.

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