Jmol and Crystal. Bob Hanson St. Olaf College, Northfield, MN

Transcription

1 Jmol and Crystal Bob Hanson St. Olaf College, Northfield, MN Crystal Workshop MSSC2018 l'università di Torino, Italia 4 Sep 2018

2 Bob Hanson St. Olaf College Jmol

3 Topics for Discussion - Jmol general introduction examples from the web general capabilities features specific to crystals

4 General Introduction to Jmol Mission: The high-quality, real-time visualization and analysis of molecular structure, dynamics, and energetics. Jmol is: open source Java cross-disciplinary actively being developed Jmol is not: a commercial enterprise a quantum computational package

5 General Introduction to Jmol Configurations: Java Application

6 General Introduction to Jmol Configurations: Java Application fast, full service, drag and drop

7 General Introduction to Jmol Configurations: Command-line Java application server-side app can run headless automated workflow.

8 General Introduction to Jmol Configurations: Command-line Java application server-side app no user interface can create images and do analyses.

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

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

11 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

12 Jmol Examples from the Web

13 Jmol Examples from the Web

14 General Capabilities of Jmol File Loading

15 General Capabilities of Jmol File Loading input configurations optimizations (all steps, or just last) vibrations, phonons molecular dynamics trajectories primitive and conventional unit cells over-ride of file-based unit cells and space groups multiple files and files with multiple structures

16 General Capabilities of Jmol File Loading since 2014 incommensurately modulated structures (3+n)D magnetic spacegroups, including (3+n)D

17 General Capabilities of Jmol File Loading incommensurately modulated structures (3+n)D magnetic spacegroups, including (3+n)D

18 General Capabilities of Jmol File Loading premade structures small molecules directly from: National Cancer Institute load $benzene PubChem load :caffeine

19 General Capabilities of Jmol File Loading premade structures crystal structures directly from: Crystallography Open Database load =cod/ (rutile SnO2) American Mineralogist Society load =ams/quartz

20 General Capabilities of Jmol Scripting - Think Python meets Molecular Flash Jmol has a rich JavaScript-like 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 200 commands. The HELP command accesses the interactive script documentation directly at

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23 General Capabilities of Jmol Output/Export Options Jmol can export a view to several formats, including: POV-Ray VRML/STL X3D animated GIF (fancy ray-tracing some people like) (can be used for 3D-printing) (XML version of VRML)

24 General Capabilities of Jmol Output/Export Options Structures can be saved in PDB, MOL, and XYZ formats. (CIF, but P1 only) Only the selected atoms are written, allowing for creating files that are subsets of the original file.

25 General Capabilities of Jmol Output/Export Options Images can be created in JPG and PNG formats. A special PNGJ format is interesting: combines an image and a ZIP file retains the full state of Jmol includes all files used in the formation of the image allows dragging the image back into the application or a web page to restore the state

26 General Capabilities of Jmol Output/Export Options Images can be created in JPG and PNG formats.

27 General Capabilities of Jmol Output/Export Options Images can be created in JPG and PNG formats.

28 General Capabilities of Jmol Output/Export Options Images can be created in JPG and PNG formats.

29 General Capabilities of Jmol Output/Export Options Images can be created in JPG and PNG formats.

30 General Capabilities of Jmol Output/Export Options Images can be created in JPG and PNG formats.

31 Try this: load tutorials/nanotube/output/test_nano03.out {3 1 1}

32 Now add: set zshade on set zshadepower 5 // removes back side of nanotube

33 Now save the structure and delete it: write PNGJ nano.png OK PNGJ C:/jmol-dev/bobtest/nano.png; quality=-1; width=642; height=452 PNGJ is a standard PNGJ image with a ZIP-file payload zap It s gone. Now, here s the cool part: Find that image on your computer and drag it back into Jmol or use CTRL- C/CTRL-V to copy and paste it into Jmol.

34 Just where you left it! Cool, eh? Because Jmol is state driven

35 Uses of PNGJ - save sessions after working on a website - transfer states from Java to/from JavaScript - create visual directories of your work - send by to collaborators - amaze your coworkers and students!

36 General Capabilities of Jmol Rendering Options ball and stick wireframe spacefill dots, stars polyhedra ellipsoids (tensors) cartoons z-shading

37 General Capabilities of Jmol Coloring Options CPK custom colors color by property {*}.temperature = {*}.vxyz.all color temperature

38 General Capabilities of Jmol Depicting vibrations arrows animation vectors on

39 Surface Capabilities of Jmol Built-in surfaces include Van der Waals and contacts (this is a ligand in a binding site, actually)

40 Surface Capabilities of Jmol Built-in surfaces include Van der Waals and contacts isosurface select {ligand} only vdw

41 Surface Capabilities of Jmol Built-in surfaces include Van der Waals and contacts contact {ligand} surface

42 Surface Capabilities of Jmol Built-in surfaces include Van der Waals and contacts contact {ligand} trimmed

43 Surface Capabilities of Jmol Built-in surfaces include Van der Waals and contacts contact {ligand} hbond

44 Surface Capabilities of Jmol Isosurface Creation from Cube Data

45 Surface Capabilities of Jmol Mappable

46 Surface Capabilities of Jmol Extensible isosurface lattice {3 3 1} xxx.cube (POV-ray output)

47 Surface Capabilities of Jmol Compressible as JVXL files write xxx.jvxl or isosurface CACHE (prior to write PNGJ xxx.png) (POV-ray output)

48 Molecule Building Jmol s modelkitmode allows for the creation and modification of models.

49 Jmol Virtual Model Kit

50 Jmol Virtual Model Kit

51 Jmol Virtual Model Kit

52 Jmol Virtual Model Kit

53 Jmol Virtual Model Kit

54 Jmol Virtual Model Kit

55 Jmol Virtual Model Kit

56 Minimization Jmol uses the Universal Force Field (UFF) to allow rapid minimization of structures.

57 Features Specific to Crystals space groups unit cells slabs and polymers tensor visualization Multipole analysis tensors as ellipsoids

58 Features Specific to Crystals space groups unit cells slabs and polymers tensor visualization Miller planes

59 Features Specific to Crystals space groups unit cells slabs and polymers tensor visualization Miller planes operator visualization

60 Features Specific to Crystals load load {1 1 1} / load { } load {1 1 1} packed / load { } load { }

61 Features Specific to Crystals load alpha_pbo.out {2 2 1} SUPERCELL {3 1 1}

62 Features Specific to Crystals brillouin zones

63 Thank you! Special thanks to: Roberto Dovesi Piero Ugliengo Bartolomeo Civalleri Pieremanuele Canepa The Jmol user group The Jmol development team