Visualization of periodic crystalline structure and wave functions using Jmol Bob Hanson St. Olaf College, Northfield, MN CCP-NC Visualization Planning Meeting Department of Materials University of Oxford May 24, 2012

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

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

General Introduction to Jmol Configurations: Application

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

Jmol Examples from the Web

Jmol Examples from the Web

Jmol Examples from the Web

Jmol Examples from the Web

Jmol Examples from the Web

Jmol Examples from the Web

Jmol Examples from the Web

Frieda Reichsman,

General Capabilities of Jmol File Loading

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

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!

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

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.

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.

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

General Capabilities of Jmol Depicting vibrations arrows animation

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

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

Surface Capabilities of Jmol Molecular Orbitals – lists and linear combinations reads basis functions linear combinations animations

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

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

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

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

Surface Capabilities of Jmol Cube/Polygon File Loading APBSKineMage CUBEMRC/CCP4 CHEM3DMSMS DSN6/OMAPOBJ EFVETPMESH JaguarPLTXPLOR/CNS JVXLXSF Isosurface cutoff 0.05 sign red blue cu.xsf.gz

Surface Capabilities of Jmol Molecular Orbitals -- Basis File Loading

Features Specific to Crystallography space groups unit cells, supercells

Features Specific to Crystallography space groups unit cells, supercells Miller planes

Features Specific to Crystallography space groups unit cells, supercells Miller planes operator visualization

Features Specific to Crystallography space groups unit cells, supercells Miller planes operator visualization ellipsoids Multipole analysis tensors as ellipsoids

Periodic Isosurface Creation from Cube Data New Capabilities of Jmol

Periodic Isosurface Creation from Cube Data (POV-ray output)

New Capabilities of Jmol contact {ligand} SURFACE

New Capabilities of Jmol contact {ligand} TRIM

New Capabilities of Jmol contact {ligand} HBOND

New Capabilities of Jmol Quaternion-Based Straightness

New Capabilities of Jmol Quaternion-Based Straightness

New Capabilities of Jmol Jmol/JSpecView

New Capabilities of Jmol Jmol/JSpecView

New Capabilities of Jmol Jmol/JSpecView

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

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

New Capabilities of Jmol load WCO6-relaxed.magres

New Capabilities of Jmol load WCO6-relaxed.magres; spacefill off; ellipsoids

New Capabilities of Jmol load T1Si3e.magres

New Capabilities of Jmol load T1Si3e.magres; spacefill off; ellipsoids

Thank you! Special thanks to: Keith Refson Jonathan Yates The Jmol user group The Jmol development team St. Olaf College Dan Kohler, St. Olaf ’10 Steven Braun, St. Olaf ‘11 Erik Wyatt, St. Olaf ’14 Andrew Hanson, Indiana U. Pierro Canepa, U. of Kent Robert Lancashire, UWI