Visualization of periodic crystalline structure and wave functions using Jmol

1. Visualization of periodic crystalline structure and wave functions using Jmol Bob Hanson St. Olaf College, Northfield, MN http://www.stolaf.edu/people/hansonr CCP-NC Visualization Planning Meeting Department of Materials University of Oxford May 24, 2012

3. Topics for Discussion • general introduction to Jmol • examples from the web • general capabilities • surface capabilities • features specific to crystallography • new capabilities • time for questions

4. General Introduction to Jmol Mission: The high-quality, real-time visualization of molecular structure, dynamics, and energetics. Jmol is: open source Java cross-disciplinary development driven by user input Jmol is not: a commercial enterprise a quantum computational package

5. General Introduction to Jmol Configurations: Application

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

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

8. Jmol Examples from the Web http://www.fiz-karlsruhe.de/icsd_web.html

9. Jmol Examples from the Web http://rruff.geo.arizona.edu/AMS/amcsd.php

10. Jmol Examples from the Web http://macxray.chem.upenn.edu

11. Jmol Examples from the Web http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse

12. Jmol Examples from the Web http://j-ice.sourceforge.net/ondemand/

13. Jmol Examples from the Web http://www.proteopedia.org

15. Frieda Reichsman, http://pubs.acs.org/doi/media/10.1021/cb600303y/figure2.htm

16. General Capabilities of Jmol File Loading

17. General Capabilities of Jmol small molecules, biomolecules crystals -- primitive or conventional unit cells 3D, 2D, and 1D periodicity vibrations, symmetry molecular dynamics trajectories multiple files and files with multiple structures minimization model building

18. General Capabilities of Jmol Scripting Jmol 12 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

21. General Capabilities of Jmol Output/Export Options Jmol can export a view to several formats, including: VRML X3D POV-Ray IDTF (for creation of U3D files for PDF documents) Maya Tachyon

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

23. General Capabilities of Jmol Output/Export Options Images can be created in 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.

24. General Capabilities of Jmol Rendering Options ball and stick wireframe spacefill dots, stars polyhedra ellipsoids cartoons symmetry

25. General Capabilities of Jmol Depicting vibrations arrows animation

26. General Capabilities of Jmol Coloring Options CPK custom colors color by property (coloring by vibrational magnitude) {*}.temperature = {*}.vxyz.all color temperature

27. Surface Capabilities of Jmol Molecular Orbitals reads basis functions linear combinations animations

28. Surface Capabilities of Jmol Molecular Orbitals – lists and linear combinations reads basis functions linear combinations animations http://chemapps.stolaf.edu/jmol/docs/examples-12/motest

29. Surface Capabilities of Jmol Built-in surfaces include Van der Waals, solvent-accessible, solvent-excluded, cavities, and molecular orbitals

30. Surface Capabilities of Jmol Built-in surfaces include Van der Waals, solvent-accessible, solvent-excluded, cavities, and molecular orbitals

31. Surface Capabilities of Jmol Built-in surfaces include Van der Waals, solvent-accessible, solvent-excluded, cavities, and molecular orbitals

32. Surface Capabilities of Jmol Built-in surfaces include Van der Waals, solvent-accessible, solvent-excluded, cavities, and molecular orbitals

33. Surface Capabilities of Jmol Cube/Polygon File Loading Isosurface cutoff 0.05 sign red blue cu.xsf.gz

34. Surface Capabilities of Jmol Molecular Orbitals -- Basis File Loading

35. Features Specific to Crystallography space groupsunit cells, supercells

36. Features Specific to Crystallography space groupsunit cells, supercellsMiller planes http://chemapps.stolaf.edu/jmol/docs/examples-12/hkl.htm

37. Features Specific to Crystallography space groupsunit cells, supercellsMiller planesoperator visualization http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse

38. Features Specific to Crystallography space groupsunit cells, supercellsMiller planesoperator visualizationellipsoids Multipole analysis tensors as ellipsoids

39. New Capabilities of Jmol Periodic Isosurface Creation from Cube Data

40. New Capabilities of Jmol Periodic Isosurface Creation from Cube Data (POV-ray output)

41. New Capabilities of Jmol contact {ligand} SURFACE

42. New Capabilities of Jmol contact {ligand} TRIM

43. New Capabilities of Jmol contact {ligand} HBOND

44. New Capabilities of Jmol Quaternion-Based Straightness

45. New Capabilities of Jmol Quaternion-Based Straightness

46. New Capabilities of Jmol Jmol/JSpecView

47. New Capabilities of Jmol Jmol/JSpecView

48. New Capabilities of Jmol Jmol/JSpecView

49. New Capabilities of Jmol load aspirin-geom-20k-vib-d3.cell

50. New Capabilities of Jmol load aspirin-geom-20k-vib-d3.cell CENTROID