ICM-Bio User Guide v.3.8

Table of contents

1 Help Videos on YouTube

2 Reference Guide

2.1 Graphics Reference Guide

2.2 ICM-Browser-Pro Reference Guide

2.3 ActiveICM Reference Guide - Create 3D Molecular Documents for the Web and PowerPoint

2.4 ICM-Chemist Reference Guide

2.5 Menu Option Guide

2.6 Tab Guide

3 Getting Started

3.1 The Basics of the Graphical User Interface

3.2 How to search and download Protein Structure, Sequences, and Chemicals

3.3 Create New Objects

3.4 Open and Read Files

3.5 Saving Files

3.6 Making Selections

3.7 Preferences

4 Protein Structure

4.1 Convert to ICM Object

4.2 Pocket Display

4.3 Crystallographic Analysis

4.4 Protein Superposition

4.5 Protein Structure Analysis

5 Molecular Graphics

5.1  Molecule Representation

5.2  Multi-Windows

5.3  Meshes - Surface - Grobs

5.4  Coloring

5.5  Lighting

5.6  3D Stereo

5.7  3D Printing

5.8  Labeling and Annotation

5.9  Display Distances and Angles

5.10 Graphics Effects

5.11 Graphics Shortcuts

5.12 Molecule Move Buttons

5.13 Clipping Tools

5.14 Graphic Layers

5.15 High Quality Publication Images

5.16 Movie Making

6 Slides & ActiveICM

6.1  Making Slides

6.2  Make a Movie from a Set of 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

6.7  ActiveICM

6.8  How to Embed in Microsoft PowerPoint 2003

6.9  How to Embed in Microsoft PowerPoint 2007

6.10 How to Embed in MicroSoft PowerPoint 2010

6.11 Embed in Web Browser

6.12 How to Use ActiveICM in PowerPoint

6.13 How to Change ActiveICM Component Properties

6.14 Advanced use of activeICM: Macros to direct visualisation changes

6.15 Background Images

6.16 ICM JavaScript (IcmJS)

7 Working with Sequences and Alignments

7.1 Read and Save Sequences

7.2 Sequence Secondary Structure

7.3 Bioinfo Menu

7.4 BLAST Search

7.5 Sequence Editor

7.6 Sequence Alignments

7.7 Alignment Editor

7.8 Color Structure and Surface by Alignment

8 Tutorials

8.1 Graphics Tutorials

8.2 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial

8.3 Protein Structure Tutorials

8.4 Sequence and Alignment Tutorials