ICM-Browser & ActiveICM Guide v.3.7-2a

Table of contents

1 Introduction

2 How To Guides and Videos

2.1 ICM-Browser How To Guide

2.2 ActiveICM How To Guide - Create 3D Molecular Documents for the Web and PowerPoint

3 Getting Started

3.1 How to Use the Graphical Display

3.2 Making Selections

3.3 Menu Option Guide

3.4 Tab Guide

4 Working with Protein Structures

4.1 Searching the PDB

4.2 Converting PDB Files Into ICM Objects

4.3 How to Display the Ligand Binding Pocket Surface and Neighboring Residues.

4.4 How to Display Hydrogen Bonds

5 Molecular Graphics

5.1  Molecule Representation

5.2  Meshes - Surface - Grobs

5.3  Coloring

5.4  Lighting

5.5  Labeling and Annotation

5.6  Display Distances and Angles

5.7  Graphics Effects

5.8  Graphics Shortcuts

5.9  Molecule Move Buttons

5.10 Clipping Tools

5.11 Graphic Layers

5.12 Make High Quality Publication Images

6 Molecular Animations, Slides, and Documents

6.1 Molecular Animations and Transitions

6.2 Making Slides

6.3 How to View and Navigate Slides

6.4 How to Edit Slides

6.5 How to Add Smooth Blending and Transition Effects Between Slides

6.6 How to Make Molecular Documents - Link HTML Text to Slides

7 ActiveICM

7.1 How to Embed in Microsoft PowerPoint 2003

7.2 How to Embed in Microsoft PowerPoint 2007

7.3 Embed in Web Browser

7.4 How to Use ActiveICM in PowerPoint

7.5 How to Change ActiveICM Component Properties

7.6 Advanced use of activeICM: Macros to direct visualisation changes

7.7 Background Images

8 Protein Superposition

8.1 Select Proteins for Superposition

8.2 Superimpose Button

9 Working with Tables

9.1 Standard ICM Tables

9.2 Molecular Tables

9.3 Insert Interactive Objects into Table Cell

9.4 Plotting Table Data

10 Tutorials

10.1 Graphics Tutorials