1. ChemAxon European UGM Visegrad 2008 Sketching and viewing with Marvin Features, tips and tricks Akos Papp

2. ChemAxon European UGM Visegrad 2008 2 Outline Main original features Main original technical features New features – 5.0 Features coming – 5.1 Future features – 5.2 Feature videos (throughout the presentation) Configurations Customization Some drawing tips and tricks Where to use keyboard for quick drawing Right click options Useful shortcuts

3. ChemAxon European UGM Visegrad 2008 3 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps

4. ChemAxon European UGM Visegrad 2008 4 Isotopes, charges, radicals

5. ChemAxon European UGM Visegrad 2008 5 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo)

6. ChemAxon European UGM Visegrad 2008 6 Stereo features

7. ChemAxon European UGM Visegrad 2008 7 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens

8. ChemAxon European UGM Visegrad 2008 8 Valence check, lone pairs

9. ChemAxon European UGM Visegrad 2008 9 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data

10. ChemAxon European UGM Visegrad 2008 10 Alias, pseudo, attached data

11. ChemAxon European UGM Visegrad 2008 11 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data Nice structures (antialiasing) Rich formatting (fonts, colors, bond thickness)

12. ChemAxon European UGM Visegrad 2008 12 Rich formatting

13. ChemAxon European UGM Visegrad 2008 13 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data Nice structures (antialiasing) Rich formatting (fonts, colors, bond thickness) Query drawing features Any atom, atom list/not-list, link nodes

14. ChemAxon European UGM Visegrad 2008 14 Any atom, atom list, link nodes

15. ChemAxon European UGM Visegrad 2008 15 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data Nice structures (antialiasing) Rich formatting (fonts, colors, bond thickness) Query drawing features Any atom, atom list/not-list, link nodes Atom properties (substitution count, aromatic, etc.)

16. ChemAxon European UGM Visegrad 2008 16 Atom properties

17. ChemAxon European UGM Visegrad 2008 17 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data Nice structures (antialiasing) Rich formatting (fonts, colors, bond thickness) Query drawing features Any atom, atom list/not-list, link nodes Atom properties (substitution count, aromatic, etc.) Bond topology (ring, chain) Reaction topology (reacting center, inversion/retention)

18. ChemAxon European UGM Visegrad 2008 18 Bond and reaction topology

19. ChemAxon European UGM Visegrad 2008 19 Main original features – 1 2D and 3D sketching and viewing Isotopes, charges, radicals, maps Stereo features (tetrahedral, double bond, diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data Nice structures (antialiasing) Rich formatting (fonts, colors, bond thickness) Query drawing features Any atom, atom list/not-list, link nodes Atom properties (substitution count, aromatic, etc.) Bond topology (ring, chain) Reaction topology (reacting center, inversion/retention) Recursive SMARTS

20. ChemAxon European UGM Visegrad 2008 20 Recursive SMARTS

21. ChemAxon European UGM Visegrad 2008 21 Main original features – 2 Markush structure drawing features

22. 22 Markush structure drawing Play feature animation: http://www.chemaxon.com/conf/Marvin08/MarkushDrawingBenzodiazepine.swf

23. ChemAxon European UGM Visegrad 2008 23 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.)

24. 24 Abbreviated groups Play feature animation: http://www.chemaxon.com/conf/Marvin08/AbbrevTosGroupCreate.swf

25. ChemAxon European UGM Visegrad 2008 25 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.) Single step reaction drawing Automatic component recognition Manual- and automapping

26. Play feature animation: http://www.chemaxon.com/conf/Marvin08/ComponentAutoRecognition.swf 26 Component autorecognition

27. Play feature animation: http://www.chemaxon.com/conf/Marvin08/Automapping.swf 27 Manual– and automapping

28. ChemAxon European UGM Visegrad 2008 28 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.) Single step reaction drawing Automatic component recognition Manual- and automapping Graphics, text boxes, electron flow arrows

29. ChemAxon European UGM Visegrad 2008 29 Electron flow arrows

30. ChemAxon European UGM Visegrad 2008 30 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.) Single step reaction drawing Automatic component recognition Manual- and automapping Graphics, text boxes, electron flow arrows 2D and 3D structure clean

31. ChemAxon European UGM Visegrad 2008 31 2D and 3D clean CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 topology 2D3D

32. ChemAxon European UGM Visegrad 2008 32 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.) Single step reaction drawing Automatic component recognition Manual- and automapping Graphics, text boxes, electron flow arrows 2D and 3D structure clean Aromatization /dearomatization

33. Play feature animation: http://www.chemaxon.com/conf/Marvin08/Aromatization.swf 33 Aromatization/dearomatization

34. ChemAxon European UGM Visegrad 2008 34 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.) Single step reaction drawing Automatic component recognition Manual- and automapping Graphics, text boxes, electron flow arrows 2D and 3D structure clean Aromatization /dearomatization Calculator plugins

35. ChemAxon European UGM Visegrad 2008 35 Calculator plugins Elemental analysis Protonation (pKa, major microsp., isoelectric point) Partitioning (logP, logD) Charge (charge, polarizability, orbital electronegativity) Isomers (tautomers, resonance, stereoisomers) Conformation (conformers, molecular dynamics) Geometry (topology analysis, geometry, polar surface area (2D), molecular surface area (3D)) H-bond donors/acc., Huckel analysis, refractivity IUPAC name generation Markush enumeration

36. ChemAxon European UGM Visegrad 2008 36 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.) Single step reaction drawing Automatic component recognition Automapping Graphics, text boxes, electron flow arrows 2D and 3D structure clean Aromatization /dearomatization Calculator plugins Multipage sketches

37. ChemAxon European UGM Visegrad 2008 37 Multipage documents

38. ChemAxon European UGM Visegrad 2008 38 Main original features – 2 Markush structure drawing features Groups Large collection of abbreviated groups Quick drawing using the keyboard Custom group creation (R-group, S-group, etc.) Single step reaction drawing Automatic component recognition Automapping Graphics, text boxes, electron flow arrows 2D and 3D structure clean Aromatization /dearomatization Calculator plugins Multipage sketches Molecule matrix view in MarvinView

39. ChemAxon European UGM Visegrad 2008 39 Molecule matrix view

40. ChemAxon European UGM Visegrad 2008 40 Main original technical features Import/export of all important molecular file formats Inter-conversion, automatic recognition

41. ChemAxon European UGM Visegrad 2008 41 File Formats Marvin CML IUPAC InChI IUPAC Name MDL Molfile Extended Molfile Rxnfile Extended Rxnfile RDfile SDfile Peptide sequence SMILES SMARTS Tripos SYBYL Mol Mol2 Gaussian Cube Gaussian Input PDB XYZ

42. ChemAxon European UGM Visegrad 2008 42 Main original technical features Import/export of all important molecular file formats Inter-conversion, automatic recognition Image export to the major image file formats

43. ChemAxon European UGM Visegrad 2008 43 Image export JPG, JPEG PNG PPM PDF SVG, SVGZ BMP EMF

44. ChemAxon European UGM Visegrad 2008 44 Main original technical features Import/export of all important molecular file formats Inter-conversion, automatic recognition Image export to the major image file formats Visualization with MarvinView and MarvinSpace

45. ChemAxon European UGM Visegrad 2008 45 MarvinView and MarvinSpace

46. ChemAxon European UGM Visegrad 2008 46 Main original technical features Import/export of all important molecular file formats Inter-conversion, automatic recognition Image export to the major image file formats Visualization with MarvinView and MarvinSpace Distributions: Standalone, JWS, Beans, Applets

47. ChemAxon European UGM Visegrad 2008 47 Beans vs. Applets Desktop applications (deployment with Installer, Java Web Start) Recommended for end-users Easy installation Recommended for developers Quick GUI building Easy customization Marvin integration into web pages Wide range of layout customization Recommended for web developers Simple web base deployment Modular architecture ensures short download time

48. ChemAxon European UGM Visegrad 2008 48 Main original technical features Import/export of all important molecular file formats Inter-conversion, automatic recognition Image export to the major image file formats Visualization with MarvinView and MarvinSpace Distributions: Standalone, JWS, Beans, Applets Pure JAVA based Platform and browser independent

49. ChemAxon European UGM Visegrad 2008 49 System compatibility Windows 95, 98, Me, NT, 2000, XP Mac OS X Unix/Linux Linux, Solaris, etc.

50. ChemAxon European UGM Visegrad 2008 50 Browser compatibility Internet Explorer Firefox Mozilla Netscape Safari Opera

51. ChemAxon European UGM Visegrad 2008 51 Main original technical features Import/export of all important molecular file formats Inter-conversion, automatic recognition Image export to the major image file formats Visualization with MarvinView and MarvinSpace Distributions: Standalone, JWS, Beans, Applets Pure JAVA based Platform and browser independent Features are available from API Additional, applet specific features

52. ChemAxon European UGM Visegrad 2008 52 Developing with Marvin Beans Additional API is accessible for Import / Export Performing calculations with plugins 2D and 3D cleaning of structures All operations accessible in the GUIs are also available in the API. Use Marvin Beans to add MarvinSketch or MarvinView as a graphical component to your standalone application

53. ChemAxon European UGM Visegrad 2008 53 Applet specific features The appropriate version for the browser / JRE is automatically selected Signed (trusted) applets enable access to local files, system clipboard and allow printing. Applet API accessible from JavaScript to fetch the current structure from the applet and send it to the server for further processing. change the structure or display options of the applet without reloading the page.

54. ChemAxon European UGM Visegrad 2008 54 Main original technical features Import/export of all important molecular file formats Inter-conversion, automatic recognition Image export to the major image file formats Visualization with MarvinView and MarvinSpace Distributions: Standalone, JWS, Beans, Applets Pure JAVA based Platform and browser independent Features are available from API Additional, applet specific features Free for Open access, non commercial websites Academic research and teaching Evaluation

55. ChemAxon European UGM Visegrad 2008 55 Major new features – 5.0 New GUI design Customizable menu Customizable toolbar

56. Play feature animation: http://www.chemaxon.com/conf/Marvin08/menucustom.swf 56 Customizable menu

57. Play feature animation: http://www.chemaxon.com/conf/Marvin08/toolbarcustom.swf 57 Customizable toolbar

58. ChemAxon European UGM Visegrad 2008 58 Major new features – 5.0 New GUI design Customizable menu Customizable toolbar ISIS/Draw-like and ChemDraw-like configurations

59. Play feature animation: http://www.chemaxon.com/conf/Marvin08/configurations.swf 59 Configurations ISIS/Draw like ChemDraw like

60. ChemAxon European UGM Visegrad 2008 60 Major new features – 5.0 New GUI design Customizable menu Customizable toolbar ISIS/Draw-like and ChemDraw-like configurations OLE component for Office documents

61. Play feature animation: http://www.chemaxon.com/conf/Marvin08/OLE.swf 61 OLE component

62. ChemAxon European UGM Visegrad 2008 62 Major new features – 5.0 New GUI design Customizable menu Customizable toolbar ISIS/Draw-like and ChemDraw-like configurations OLE component for Office documents Periodic system Query tab containing Generic query features and periodic table groups

63. ChemAxon European UGM Visegrad 2008 63 Periodic table Query tab

64. ChemAxon European UGM Visegrad 2008 64 Major new features – 5.0 New GUI design Customizable menu Customizable toolbar ISIS/Draw-like and ChemDraw-like configurations OLE component for Office documents Periodic system Query tab containing Generic query features and periodic table groups Dynamic IUPAC name text box

65. ChemAxon European UGM Visegrad 2008 65 Dynamic IUPAC name

66. ChemAxon European UGM Visegrad 2008 66 Major new features – 5.0 New GUI design Customizable menu Customizable toolbar ISIS/Draw-like and ChemDraw-like configurations OLE component for Office documents Periodic system Query tab containing Generic query features and periodic table groups Dynamic IUPAC name text box Creating templates by drag-drawing to toolbar

67. Play feature animation: http://www.chemaxon.com/conf/Marvin08/template_rovid.swf 67 Drag&drop to MyTemplates

68. ChemAxon European UGM Visegrad 2008 68 Major new features – 5.0 New GUI design Customizable menu Customizable toolbar ISIS/Draw-like and ChemDraw-like configurations OLE component for Office documents Periodic system Query tab containing Generic query features and periodic table groups Dynamic IUPAC name text box Creating templates by drag-drawing to toolbar Spreadsheet-like view in MarvinView for SD and RDfiles

69. ChemAxon European UGM Visegrad 2008 69 Spreadsheet view

70. ChemAxon European UGM Visegrad 2008 70 Minor new features – 5.0 Multicenter atom Position variation bond Coordinate bond

71. Play feature animation: http://www.chemaxon.com/conf/Marvin08/Ferrocene.swf 71 Multicenter, coordinate bond

72. ChemAxon European UGM Visegrad 2008 72 Minor new features – 5.0 Multicenter atom Position variation bond Coordinate bond Generalized placement of groups and templates Shift button changes between expanded and contracted form of groups when placing to the canvas (since 5.0.3) Chain drawing displays the last carbon number New group types Repeating unit, monomer, polymer, generic, etc. Improved quality both in 2D and 3D clean Recent file list Markush structure specific Zoom to scaffold and r-group lists

73. Play feature animation: http://www.chemaxon.com/conf/Marvin08/MarkushZoomTo.swf 73 Zoom to scaffold or R–group

74. ChemAxon European UGM Visegrad 2008 74 Features coming – 5.1 Accelerated initialization of Marvin at startup Name to structure conversion Importing IUPAC names through the source On the fly conversion of names pasted to the canvas Opening.name files Printing redesign Print preview Print to PDF Structure preview (optional) on the file open dialog window Browsing capability in multistructure files

75. Play feature animation: http://www.chemaxon.com/conf/Marvin08/StructurePreview.swf 75 Structure preview

76. ChemAxon European UGM Visegrad 2008 76 Future features – 5.2 Transparent structure drawing Multistep reaction support Real arrows with automatic assignment of reactants MarvinView GUI redesign Structure checker component Copy/Cut/Paste/(Ctrl+)Drag(&Drop) redesign CDX (ChemDraw) file import/export Load templates from specified directories New Markush related features Enhanced handling of group attachment points Dynamic font size change

77. ChemAxon European UGM Visegrad 2008 Questions?

78. ChemAxon European UGM Visegrad 2008 Thank you for your attention! For more information please visit www.chemaxon.com