ICM-Browser-Pro User Guide v.3.7-3b

Table of contents

1 Introduction

2 How To Guides and Videos

2.1 ICM-Browser How To Guide

2.2 ICM-Browser-Pro How To Guide

2.3 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 How to Embed in MicroSoft PowerPoint 2010

7.4 Embed in Web Browser

7.5 How to Use ActiveICM in PowerPoint

7.6 How to Change ActiveICM Component Properties

7.7 Advanced use of activeICM: Macros to direct visualisation changes

7.8 Background Images

8 Movie Making

9 Protein Structure Analysis

9.1  Find Related Chains

9.2  Calculate RMSD

9.3  Contact Areas

9.4  Identify Closed Cavities

9.5  Surface Area

9.6  Measure Distances

9.7  Planar Angle

9.8  Dihedral Angle

9.9  Ramachandran Plot Interactive

9.10 Export Ramachandran Plot

10 Protein Superposition

10.1 Select Proteins for Superposition

10.2 Superimpose Button

10.3 Superimpose by 3D

10.4 Superimpose Multiple Proteins

10.5 Arrange as Grid

10.6 Superimpose Sites by Atomic Property Fields

11 Crystallographic Analysis

11.1 Crystallographic Neighbor

11.2 Crystallographic Cell

11.3 Biomolecule Generator

11.4 Get Electron Density Map

11.5 Map's Original Cell

11.6 Contour Electron Density Map

11.7 Convert Xray Density to Grid

12 Working with Tables

12.1 Standard ICM Tables

12.2 Molecular Tables

12.3 Insert Interactive Objects into Table Cell

12.4 Plotting Table Data

13 ICM in KNIME

14 Tutorials

14.1 Graphics Tutorials