1. Cloud-Based Visualization of Value-Added Model Annotations Using Jmol Bob Hanson St. Olaf College, Northfield, MN http://www.stolaf.edu/people/hansonr University of Dundee Dundee, Scotland 2015.7.20

4. General Introduction to Jmol Mission: The high-quality, real-time visualization of molecular structure, dynamics, and energetics. open source Java cross-disciplinary development driven by user input

5. General Introduction to Jmol small molecules biomolecules PDB, PQR, PyMOL, many other file formats molecular dynamics trajectories multiple files and files with multiple structures automatic addition of hydrogen atoms MMFF94 and UFF minimization model building

6. Jmol reads 60+ file model file formats, including PyMOL PSE Jaim Prilusky http://ispcsrv.weizmann.ac.il/a2jmolb/browse General Introduction to Jmol

7. General Capabilities of Jmol Output/Export Options Structures can be saved in PDB, MOL, XYZ, and JSON formats. Only the selected atoms are output, allowing for creating files that are subsets of the original file.

8. General Capabilities of Jmol Output/Export Options Images can be created in high-quality JPG and PNG formats. These images retain the full state of Jmol, allowing dragging of the image back into the application of signed applet to restore the state. In addition, special formats PNGJ and JMOL retain, along with the script, the entire set of files used.

9. General Introduction to Jmol Scripting Jmol has a rich scripting language that is easily accessed via a console, a pop-up menu, or via an API. There are nearly 2000 semantic tokens and about 150 commands. The HELP command accesses the interactive script documentation; VERY active and friendly user group! http://chemapps.stolaf.edu/jmol/docs

12. General Introduction to Jmol Scripting Jmol’s scripting language is extensible function loadPDB(xxxx, ext) { load @{“*“+xxxx + (ext ? “/” + ext : “”)} select protein or nucleic cartoons only; color structure select * } loadpdb “1crn”

13. General Introduction to Jmol Configurations: Application

14. General Introduction to Jmol Configurations: Java Applet easily added highly customizable highly interactive highly modular signed or unsigned in 20 languages

15. General Introduction to Jmol Configurations: JavaScript App identical to Java works in all popular browsers, including Safari for the iPad, android phones, etc. somewhat slower than Java

16. Jmol Examples from the Web http://www.rcsb.org

17. Jmol Examples from the Web

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

19. Surfaces Electron Density Mesh

20. Surfaces Van der Waals and “solvent-accessible” representations

21. Surfaces Numerical data can be mapped onto atoms and surfaces for visualization

22. Surfaces Numerical data can be mapped onto surfaces for visualization, or used to change atom properties, such as displayed atom radius

23. Contact Mapping contact {ligand} SURFACE

24. Contact Mapping contact {ligand} TRIM

25. Contact Mapping contact {ligand} TRIM

26. Contact Mapping contact {ligand} HBOND

27. Contact Mapping

29. Annotations Models are more than atom positions. Approximations Constraints Ambiguity Correlations

30. Annotations The future is in combining data from various sources.

31. Annotations The future is in combining data from various sources.

32. Annotations The future is in combining data from various sources. load =1d66

33. Annotations The future is in combining data from various sources. load =1d66 cartoons only

34. Annotations The future is in combining data from various sources. load =1d66 cartoons only color structure

35. Annotations Visualizing validation data load =4tvj/val cartoons only color structure

36. Annotations Visualizing validation data load =4tvj/val cartoons only color structure

37. Annotations Visualizing validation data load =4tvj/val

38. Annotations Visualizing validation data load =4tvj/val color property_rsrz

39. Annotations Visualizing validation data load =4tvj/val {*}.radius = {*}.property_clashes.all

40. Annotations Visualizing validation data load =4tvj/val color property_clashes contact {Lys325} {Thr323}

41. Annotations Visualizing validation data load =2bxa/val; wireframe only select property_rsrz > 3; wireframe 0.2 Isosurface “=2bxa”

42. Annotations JSON format from EBI A simple RESTful call Fully generalizable JSON code (shown here using pretty=true) load =4tvj/val

43. Annotations - Domains =xxxx/dom or *xxxx/dom

44. Annotations - Domains =xxxx/dom or *xxxx/dom

45. Annotations - Domains =xxxx/dom or *xxxx/dom

46. Annotations - Domains

47. http://www.ebi.ac.uk/pdbe/api/mappings/1lyd?pretty=true&metadata=true

48. Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

49. Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

50. Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

51. Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

52. Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

53. Summary We now have ready access to a wide variety of metadata relating to biomolecules. You can think of a model with annotations as a mini “database” that can be queried. Jmol is at the forefront of integration of these services into molecular visualization. Any JSON-based data can be incorporated.

54. Thank you! Geoff Barton, Jim Proctor, Mungo Carstairs Jmol User Community St. Olaf College Larson-Anderson Endowment Fund

55. Thank You! Geoff Barton, Jim Procter Mungo Carstairs Jmol User Community St. Olaf College Larson-Anderson Endowment Fund