Visualization of periodic crystalline structure and wave functions using Jmol

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


Configurations:

Application


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


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


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


http://macxray.chem.upenn.edu


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


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


http://www.proteopedia.org

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

General Capabilities of Jmol

File Loading


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


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


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



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.



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.


Rendering Options

ball and stick

wireframe

spacefill

dots, stars

polyhedra

ellipsoids

cartoons

symmetry


Depicting vibrations

arrows

animation


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


Molecular Orbitals – lists and linear combinations

reads basis functions

linear combinations

animations

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


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


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


Molecular Orbitals -- Basis File Loading

Features Specific to Crystallography

space groupsunit cells, supercells


space groupsunit cells, supercellsMiller planes

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


space groupsunit cells, supercellsMiller planesoperator visualization

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


space groupsunit cells, supercellsMiller planesoperator visualizationellipsoids

Multipole analysis tensors as ellipsoids

Periodic Isosurface Creation from Cube Data

New Capabilities of Jmol


Periodic Isosurface Creation from Cube Data

(POV-ray output)


contact {ligand} SURFACE


contact {ligand} TRIM


contact {ligand} HBOND


Quaternion-Based Straightness


Jmol/JSpecView


load aspirin-geom-20k-vib-d3.cell


load aspirin-geom-20k-vib-d3.cell CENTROID


load WCO6-relaxed.magres


load WCO6-relaxed.magres; spacefill off; ellipsoids


load T1Si3e.magres


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

Visualization of periodic crystalline structure and wave functions using Jmol

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