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Jmol virtual model kit: An entirely new way to build and explore molecular structures

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.

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Jmol virtual model kit: An entirely new way to build and explore molecular structures

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  1. 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

  2. Thanks for the greatcollaboration! Otis Rothenberger Tom Newton

  3. 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

  4. 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!

  5. The Jmol Applet Peter Rose, RCSB http://www.rcsb.org/pdb/explore/jmol.do?structureId=1LDN

  6. Alan Hewat, http://icsd.fiz-karlsruhe.de/icsd/

  7. Alan Hewat, http://icsd.fiz-karlsruhe.de/icsd/

  8. Bob Hanson, http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm

  9. Bob Hanson, http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm

  10. The Molecular Workbench Charles Xie, Concord Consortium http://mw.concord.org/modeler/

  11. Standard Jmol Input and Display Capability 3D Coordinate File Jmol Example Coordinate/Data Formats MDL Molfile mol Protein Data Bank pdb SPARTAN spartan JME Editor jme Structure Data Format sdf MEP Calculated from sdf Data HOMO Calculated from spartan Data

  12. Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest

  13. Molecular Orbitals (Including Linear Combinations) http://chemapps.stolaf.edu/jmol/docs/examples-12/motest

  14. What’s the logical next step?

  15. A Model Kit http://www.indigo.com/models/molecular-models.html

  16. A Model Kit Instructive http://www.indigo.com/models/molecular-models.html

  17. A Model Kit InstructiveBasic geometry http://www.indigo.com/models/molecular-models.html

  18. A Model Kit InstructiveBasic geometryFun! http://www.indigo.com/models/molecular-models.html

  19. Jmol Virtual Model Kit

  20. Jmol Virtual Model Kit

  21. Jmol Virtual Model Kit

  22. Jmol Virtual Model Kit

  23. Jmol Virtual Model Kit

  24. Jmol Virtual Model Kit

  25. Jmol Virtual Model Kit

  26. Jmol Virtual Model Kit

  27. Jmol Virtual Model Kit

  28. Jmol Virtual Model Kit

  29. Jmol Virtual Model Kit

  30. Jmol Virtual Model Kit

  31. Jmol Virtual Model Kit set modelKitMode

  32. CheMagic O=Chem VMK http://chemagic.com/web_molecules

  33. CheMagic O=Chem VMK Structure Drawing http://chemagic.com/web_molecules

  34. Jmol/JME Information Flow Student draws JME (2D) Jmol (3D) 2D coord optimize view compare

  35. Jmol/JME Information Flow Student draws JME (2D) Jmol (3D) SMILES SMILES vs. compare

  36. Jmol/JME Information Flow Student draws JME (2D) Jmol (3D) SMILES Student’s drawn structure compared with key SMILES vs. compare CCC(Br)C C[C@@H](Br)CC

  37. Jmol/JME Information Flow Student draws JME (2D) Jmol (3D) SMILES Student’s drawn structure compared with key SMILES vs. compare “Please indicate the stereochemistry.” CCC(Br)C C[C@@H](Br)CC

  38. 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

  39. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference)

  40. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) Do these atoms have the correct connectivity (and absolute stereochemistry)?

  41. Jmol Find/Compare Capabilities {*}.find(“SMILES”, SMILES_reference) Do these atoms have the correct connectivity (and absolute stereochemistry)? {*}.find("SMARTS",SMARTS_reference)

  42. 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)?

  43. 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”)

  44. 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?

  45. 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”)

  46. 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?

  47. CheMagic O=Chem VMK Molecular Editor http://chemagic.com/web_molecules

  48. Chemical Identifier Resolver NIH: NCI/CADD Group Web Resource “representation” “identifier” /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) chemical names CAS numbers *SMILES strings IUPAC InChI/InChIKeys NCI/CADD IdentifiersCACTVS HASHISYNSC number *molfile NIH Resolver * Spoken by Jmol Markus Sitzmann http://cactus.nci.nih.gov/chemical/structure

  49. Jmol/NIH Information Flow Student types “tylenol” This model kit is special! Jmol (3D)

  50. Jmol/NIH Information Flow Student types “tylenol” This model kit is special! Jmol (3D)

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