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

ChemAxon European UGM Visegrad 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

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

ChemAxon European UGM Visegrad Isotopes, charges, radicals

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

ChemAxon European UGM Visegrad Stereo features

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Valence check, lone pairs

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Alias, pseudo, attached data

ChemAxon European UGM Visegrad 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)

ChemAxon European UGM Visegrad Rich formatting

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Any atom, atom list, link nodes

ChemAxon European UGM Visegrad 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.)

ChemAxon European UGM Visegrad Atom properties

ChemAxon European UGM Visegrad 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)

ChemAxon European UGM Visegrad Bond and reaction topology

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Recursive SMARTS

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

22 Markush structure drawing Play feature animation:

ChemAxon European UGM Visegrad 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 Abbreviated groups Play feature animation:

ChemAxon European UGM Visegrad 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

Play feature animation: 26 Component autorecognition

Play feature animation: 27 Manual– and automapping

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Electron flow arrows

ChemAxon European UGM Visegrad 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

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

ChemAxon European UGM Visegrad 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

Play feature animation: 33 Aromatization/dearomatization

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Multipage documents

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Molecule matrix view

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

ChemAxon European UGM Visegrad 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

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

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

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad MarvinView and MarvinSpace

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad 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

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

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

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad 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.

ChemAxon European UGM Visegrad 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

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

Play feature animation: 56 Customizable menu

Play feature animation: 57 Customizable toolbar

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

Play feature animation: 59 Configurations ISIS/Draw like ChemDraw like

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

Play feature animation: 61 OLE component

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Periodic table Query tab

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Dynamic IUPAC name

ChemAxon European UGM Visegrad 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

Play feature animation: 67 Drag&drop to MyTemplates

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad Spreadsheet view

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

Play feature animation: 71 Multicenter, coordinate bond

ChemAxon European UGM Visegrad 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

Play feature animation: 73 Zoom to scaffold or R–group

ChemAxon European UGM Visegrad 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

Play feature animation: 75 Structure preview

ChemAxon European UGM Visegrad 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

ChemAxon European UGM Visegrad 2008 Questions?

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