June, 2007 David Spender*, Erika Biró What's new in Marvin and development discussion

Contents Whats new in Marvin? Structure representation Better quality graphics Improved usability New GUI design Plug-ins File IO Future plans and discussion

Structure representation Improvements in Markush compound drawing (alpha) –Position variation –Repeating unit with repetition ranges

Structure representation Coordination compounds (alpha) –New bond type: coordinate bond Between atom – atom: Between atom – group of atoms: –Connection to a group of atoms with multicenter attachment point Click here for movie

Structure representation –Ferrocene, metallocene examples: Click here for movie

Structure representation Polymer drawing (alpha) –Source and structure-based representation of polymer types: SRU, repeating unit with repetition ranges, anypolymer, copolymer, crosslink, graft, mer, modification, monomer

Drawing of ordered and unordered mixtures (release 4.1.2) Structure representation

Multistep reaction drawing (alpha) – Reaction scheme with any number and layout of graphical reaction arrows

Left and right abbreviations for abbreviated groups (release 4.1) Better quality graphics Click here for movie

Better quality graphics Improved 2D cleaning (alpha) –Nice cleaning of big rings (built up from hexagons) –Template based OldNew

Better quality graphics OldNew

Better quality graphics New graphical objects –Graphical arrow in reaction (release 4.1.8) –Graphical brackets (alpha)

Improved usability Status bar with 2D/3D drawing mode selection and modified status (alpha) Chain drawing mode button (alpha)

Improved usability Insertable OLE component into MSOffice documents (alpha)

New GUI design Customizable menus and toolbar (alpha) Customizable shortcut keys (alpha) Three ways of customization (alpha) : –Interactive –Configuration file –API

New GUI design Toolbar and menubar icons Cross-platform Java Look (JGoodies) Improved User Interface design and usability Java Feel (coming soon)

New GUI design Sample default layout demonstrating graphics design

New GUI design Customization...

New GUI design Toolbar icon sizes are customized Appearing actions are customized Menu is reorganized by creating a new custom menu Sample customized layout

Plug-ins Tautomerization Calculator Plugin: –Generation of the major (dominant) tautomeric forms based on predicted pKa values. (release 4.1) –Generation of the canonic tautomeric form based on predicted pKa and an empirical rule system. Filtering of tautomer couples. (release 4.1.9) –Prediction of the tautomer distribution. (release 4.1.9)

Plug-ins –The length of the tautomerization path can optionally be adjusted. (release 4.1.9) –Takes into account the major tautomeric form in the pKa, logP, and the logD calculations. (release 4.2) Markush enumeration Calculator Plugin (alpha) Structure to name Calculator Plugin (release 4.1.7) –Traditional or IUPAC name

Plug-ins –Name generation is free when used from Marvin GUI. –Real-time updated name display in MarvinSketch (alpha) Click here for movie

File IO Saving of specific Marvin settings, stored in mrv with structure (alpha) PDB import improvements, for example multi-model proteins (release 4.1.2)

Future plans and discussion Basic structural IO of CDX (ChemDraw) format Align & distribute for molecules in MarvinSketch Load Templates from specified directories Spreadsheet-like table where different columns store different types of data

Future plans and discussion Name to structure New skins for Marvin to help chemists who are used to other programs like ChemDraw and Isis/Draw.