Jmol virtual model kit: An
entirely new way to build and
explore molecular structures
Robert M. Hanson, Otis Rothenberger, Thomas Newton
241st National Meeting of the American Chemical Society
Anaheim, California
March 28, 2011
Thanks for the great
collaboration!
Otis Rothenberger
Tom Newton
The Jmol Project
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•
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Jmol molecular visualization project
Open-source
Jmol.sourceforge.net
Active user/developer community
about 400 “users”
about 150 “developers”
collectively 23,000 list messages
The Jmol Project
•
•
•
•
Jmol molecular visualization project
Open-source
Jmol.sourceforge.net
Active user/developer community
about 400 “users”
about 150 “developers”
collectively 23,000 list messages
This means YOU!
The Jmol Applet
Peter Rose, RCSB http://www.rcsb.org/pdb/explore/jmol.do?structureId=1LDN
Alan Hewat, http://icsd.fiz-karlsruhe.de/icsd/
Alan Hewat, http://icsd.fiz-karlsruhe.de/icsd/
Bob Hanson, http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm
Bob Hanson, http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm
The Molecular Workbench
Charles Xie, Concord Consortium http://mw.concord.org/modeler/
Standard Jmol Input and Display Capability
3D
Coordinate
File
Jmol
Example Coordinate/Data Formats
MDL Molfile
mol
Protein Data Bank
pdb
SPARTAN
spartan
MEP Calculated from sdf Data
JME Editor
jme
Structure Data Format
sdf
HOMO Calculated from spartan Data
Molecular Orbitals
(Including Linear Combinations)
http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
Molecular Orbitals
(Including Linear Combinations)
http://chemapps.stolaf.edu/jmol/docs/examples-12/motest
What’s the logical next step?
A Model Kit
http://www.indigo.com/models/molecular-models.html
A Model Kit
Instructive
http://www.indigo.com/models/molecular-models.html
A Model Kit
Instructive
Basic geometry
http://www.indigo.com/models/molecular-models.html
A Model Kit
Instructive
Basic geometry
Fun!
http://www.indigo.com/models/molecular-models.html
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
Jmol Virtual Model Kit
set modelKitMode
CheMagic O=Chem VMK
http://chemagic.com/web_molecules
CheMagic O=Chem VMK
Structure Drawing
http://chemagic.com/web_molecules
Jmol/JME Information Flow
Student
draws
JME (2D)
2D coord
Jmol (3D)
optimize
view
compare
Jmol/JME Information Flow
Student
draws
JME (2D)
SMILES
Jmol (3D)
SMILES
vs.
compare
Jmol/JME Information Flow
Student
draws
SMILES
JME (2D)
Student’s drawn structure
compared with key
vs.
CCC(Br)C
Jmol (3D)
SMILES
compare
C[C@@H](Br)CC
Jmol/JME Information Flow
Student
draws
SMILES
JME (2D)
Student’s drawn structure
compared with key
vs.
Jmol (3D)
SMILES
compare
“Please indicate the stereochemistry.”
CCC(Br)C
C[C@@H](Br)CC
Jmol/JME Information Flow
Student
Jmol can compare natively
either SMILES (connections and
stereochemistry) or 3D
coordinates (connections,
stereochemistry, conformation)
creates
Jmol (3D)
3D or SMILES
compare
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Do these atoms have the correct connectivity (and absolute stereochemistry)?
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Do these atoms have the correct connectivity (and absolute stereochemistry)?
{*}.find("SMARTS",SMARTS_reference)
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Do these atoms have the correct connectivity (and absolute stereochemistry)?
{*}.find("SMARTS",SMARTS_reference)
Does this model contain this substructure (possibly including stereochemistry)?
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Do these atoms have the correct connectivity (and absolute stereochemistry)?
{*}.find("SMARTS",SMARTS_reference)
Does this model contain this substructure (possibly including stereochemistry)?
compare({model1}, {model2}, “ISOMER”)
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Do these atoms have the correct connectivity (and absolute stereochemistry)?
{*}.find("SMARTS",SMARTS_reference)
Does this model contain this substructure (possibly including stereochemistry)?
compare({model1}, {model2}, “ISOMER”)
Are model1 and model2 identical, enantiomers, diasteriomers,
constitutional isomers, or none of the above?
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Do these atoms have the correct connectivity (and absolute stereochemistry)?
{*}.find("SMARTS",SMARTS_reference)
Does this model contain this substructure (possibly including stereochemistry)?
compare({model1}, {model2}, “ISOMER”)
Are model1 and model2 identical, enantiomers, diasteriomers,
constitutional isomers, or none of the above?
compare(SMILES1, SMILES2, “ISOMER”)
Jmol Find/Compare Capabilities
{*}.find(“SMILES”, SMILES_reference)
Do these atoms have the correct connectivity (and absolute stereochemistry)?
{*}.find("SMARTS",SMARTS_reference)
Does this model contain this substructure (possibly including stereochemistry)?
compare({model1}, {model2}, “ISOMER”)
Are model1 and model2 identical, enantiomers, diasteriomers,
constitutional isomers, or none of the above?
compare(SMILES1, SMILES2, “ISOMER”)
Are SMILES1 and SMILES2 identical, enantiomers, diasteriomers,
constitutional isomers, or none of the above?
CheMagic O=Chem VMK
Molecular Editor
http://chemagic.com/web_molecules
Chemical Identifier Resolver
NIH: NCI/CADD Group Web Resource
“representation”
“identifier”
chemical names
CAS numbers
*SMILES strings
IUPAC InChI/InChIKeys
NCI/CADD Identifiers
CACTVS HASHISY
NSC number
*molfile
NIH
Resolver
/SMILES
/names, /iupac_name
/cas
/inchi, /stdinchi
/inchikey, /stdinchikey
/ficts, /ficus, /uuuuu
/image
/file, /sdf
/mw, /monoisotopic_mass
/formula
/twirl, /3d (Just for Fun)
/urls (Possibilities)
* Spoken by Jmol
Markus Sitzmann
http://cactus.nci.nih.gov/chemical/structure
Jmol/NIH Information Flow
Student
types
“tylenol”
This model kit is special!
Jmol (3D)
Jmol/NIH Information Flow
Student
types
“tylenol”
This model kit is special!
Jmol (3D)
Jmol/NIH Information Flow
Student
types
“tylenol”
This model kit is special!
Jmol (3D)
SDF file
“tylenol”
NIH Resolver
Jmol/NIH Information Flow
This model kit is special!
load “$tylenol”
Jmol (3D)
SDF file
“tylenol”
NIH Resolver
http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True
Jmol/NIH Information Flow
Identifier can be a chemical name, a SMILES string, a CAS
registry number, an INCHI key, or many other formats
This model kit is special!
load “$tylenol”
Jmol (3D)
SDF file
“tylenol”
NIH Resolver
http://cactus.nci.nih.gov/chemical/structure/tylenol/file?format=sdf&get3d=True
CheMagic O=Chem VMK
Model Tools
http://chemagic.com/web_molecules
CheMagic O=Chem VMK
Social Network
JME
Jmol
NIH Resolver
CheMagic
NIST
Webbook
nmrdb.org
http://chemagic.com/web_molecules
PubChem
nmrdb.org
One more development…
What do you think this displays?
<html>
<body>
<h3>Acetaminaphen is one of my favorite medications.</h3>
<br />
<script type="text/javascript" language="JavaScript"
src="http://chemagic.com/web_molecules/jmolmodel.aspx?model=tylenol&width=300&height=300">
</script>
</body>
</html>
Jmol molecular “Widget”
Jmol molecular “Widget”
<script type="text/javascript" language="JavaScript"
src="http://chemagic.com/web_molecules/jmolmodel.aspx?model=tylenol&width=300&height=300">
</script>
Thank you!