Visualization of periodic crystalline structure and wave functions

using Jmol

Bob HansonSt. Olaf College, Northfield, MN

http://www.stolaf.edu/people/hansonr

CCP-NC Visualization Planning MeetingDepartment of Materials

University of OxfordMay 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

http://www.rcsb.org

Jmol Examples from the Web

http://www.fiz-karlsruhe.de/icsd_web.html

Jmol Examples from the Web

http://rruff.geo.arizona.edu/AMS/amcsd.php

Jmol Examples from the Web

http://macxray.chem.upenn.edu

Jmol Examples from the Web

http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse

Jmol Examples from the Web

http://j-ice.sourceforge.net/ondemand/

Jmol Examples from the Web

http://www.proteopedia.org

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

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!

http://chemapps.stolaf.edu/jmol/docs

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.allcolor 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

http://chemapps.stolaf.edu/jmol/docs/examples-12/motest

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

APBS KineMage

CUBE MRC/CCP4

CHEM3D MSMS

DSN6/OMAP OBJ

EFVET PMESH

JaguarPLT XPLOR/CNS

JVXL XSF

Isosurface cutoff 0.05 sign red blue cu.xsf.gz

Surface Capabilities of Jmol

Molecular Orbitals -- Basis File Loading

Features Specific to Crystallography

space groupsunit cells, supercells

Features Specific to Crystallography

space groupsunit cells, supercellsMiller planes

http://chemapps.stolaf.edu/jmol/docs/examples-12/hkl.htm

Features Specific to Crystallography

space groupsunit cells, supercellsMiller planesoperator visualization

http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse

Features Specific to Crystallography

space groupsunit cells, supercellsMiller planesoperator visualizationellipsoids

Multipole analysis tensors as ellipsoids

Periodic Isosurface Creation from Cube Data

New Capabilities of Jmol

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 ’10Steven Braun, St. Olaf ‘11Erik Wyatt, St. Olaf ’14

Andrew Hanson, Indiana U.Pierro Canepa, U. of KentRobert Lancashire, UWI