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
Topics for Discussion
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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.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
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 groups
unit cells, supercells
Features Specific to Crystallography
space groups
unit cells, supercells
Miller planes
http://chemapps.stolaf.edu/jmol/docs/examples-12/hkl.htm
Features Specific to Crystallography
space groups
unit cells, supercells
Miller planes
operator visualization
http://chemapps.stolaf.edu/jmol/docs/examples-11/jcse
Features Specific to Crystallography
space groups
unit cells, supercells
Miller planes
operator visualization
ellipsoids
Multipole analysis tensors as ellipsoids
New Capabilities of Jmol
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!
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
Special thanks to:
Keith Refson
Jonathan Yates
The Jmol user group
The Jmol development team
St. Olaf College