MarvinSketch User's Guide

Table of Contents

• Introduction to MarvinSketch
• Installation/System Requirements
• Application Instructions
• License Management
• Quick Help
• MarvinSketch Graphical User Interface
• Canvas
• Menus
• Toolbars
• Pop-up Menus
• Status Bar
• Dialogs
• Shortcuts
• Customizing MarvinSketch
• Configurations of MarvinSketch
• Customizing MarvinSketch - Server side
• Basic MarvinSketch Functions
• File Formats
• Cut/Copy/Paste and Drag & Drop Functionality
• Create a new molecule
• Open an existing molecule file
• Save molecule
• Print
• Drawing structures
  • Atoms
  • Bonds
  • Templates
  • Coordination compounds
  • Markush structures
  • Flip a molecule
  • Mirror a molecule
• Reactions
• Drawing R-group queries
• Draw S-groups
• Drawing graphics and text boxes
• Drawing Link atoms
• Selecting structures
• Deleting structures
• Working with structures
  • Visually editing the structure
  • Editing the Source
  • Cleaning
  • Aromatic rings
• Stereochemistry
• Structure Display Options
  • Moving and Rotating
  • Scaling
  • Molecule Format
  • Colors
  • Implicit/Explicit Hydrogens
  • Error Highlighting
• Launching 2D and 3D Viewers
• Customizing structure drawing styles
• Chemical Features of MarvinSketch
• Valence Check
• Charges
• Reactions
• Mapping
• Isotopes
• E/Z feature
• S-groups
• Link Nodes
• Working with Groups
• Working with Radicals
• Query Guide
  • R-groups
  • Atom Lists
  • Not Lists
  • Generic Atoms
  • Atom Properties
• Calculator Plugins
• Elemental Analysis Plugin
• IUPAC Naming Plugin
• Protonation
  • pK_a Plugin
  • Major Microspecies Plugin
  • Isoelectric Point Plugin
• Partitioning
  • logP Plugin
  • logD Plugin
• Charge
  • Charge Plugin
  • Polarizability Plugin
  • Orbital Electronegativity Plugin
• Isomers
  • Tautomerization Plugin
  • Resonance Plugin
  • Stereoisomer Plugin
• Conformation
  • Conformer Plugin
  • Molecular Dynamics Plugin
• Geometry
  • Topology Analysis Plugin
  • Geometry Plugin
  • Polar Surface Area Plugin (2D)
  • Molecular Surface Area Plugin (3D)
• Markush Enumeration Plugin
• Other
  • Hydrogen Bond Donor-Acceptor Plugin
  • Huckel Analysis Plugin
  • Refractivity Plugin
• Test Results
• References
• Acknowledgements

Marvin User's Guide

Copyright © 1998-2009 ChemAxon Ltd.

http://www.chemaxon.com/marvin