Transcript acs-03-2011-jmolModelKit
Jmol virtual model kit: An entirely new way to build and explore molecular structures
Robert M. Hanson, Otis Rothenberger, Thomas Newton 241 st National Meeting of the American Chemical Society Anaheim, California March 28, 2011
Thanks for the great collaboration!
Otis Rothenberger Tom Newton
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
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
MDL Molfile
mol
Example Coordinate/Data Formats
Protein Data Bank
pdb
MEP Calculated from sdf Data
SPARTAN
spartan
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
set modelKitMode Jmol Virtual Model Kit
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 optimize
Jmol (3D)
view compare
Jmol/JME Information Flow
Student draws SMILES
JME (2D) Jmol (3D)
vs.
SMILES compare
Jmol/JME Information Flow
Student draws
JME (2D)
Student’s drawn structure compared with key vs.
SMILES CCC(Br)C C[C@@H](Br)CC
Jmol (3D)
SMILES compare
Jmol/JME Information Flow
Student draws SMILES
JME (2D) Jmol (3D)
Student’s drawn structure compared with key CCC(Br)C vs.
C[C@@H](Br)CC SMILES compare “Please indicate the stereochemistry.”
Jmol/JME Information Flow Jmol can compare natively either SMILES (connections and stereochemistry) or 3D coordinates (connections, stereochemistry, conformation)
Student 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 “identifier”
chemical names
CAS numbers
*SMILES strings IUPAC InChI/InChIKeys
NCI/CADD Identifiers CACTVS HASHISY NSC number
*molfile
NIH Resolver “representation”
/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
Jmol CheMagic O=Chem VMK Social Network JME NIH Resolver CheMagic NIST Webbook nmrdb.org
http://chemagic.com/web_molecules PubChem
nmrdb.org
One more development…
What do you think this displays?