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

2.4 ICM-Chemist How To Guide

2.5 ICM-Chemist-Pro How To Guide

3 Getting Started

3.1 How to Use the Graphical Display

3.2 Making Selections

3.3 How to Work With Sequences and Alignments

3.4 How to work with Protein Structures

3.5 Menu Option Guide

3.6 Tab Guide

4 Molecular Graphics

4.1  Molecule Representation

4.2  Coloring

4.3  Lighting

4.4  Labeling and Annotation

4.5  Display Distances and Angles

4.6  Visual Effects

4.7  Graphics Shortcuts

4.8  Molecule Move Buttons

4.9  Clipping Tools

4.10 Graphic Layers

4.11 Make High Quality Publication Images

5 Making Molecular Animations, Slides, and Documents

5.1 Molecular Animations and Transitions

5.2 Making Molecular Slides

5.3 How to View and Navigate Slides

5.4 How to Edit Slides

5.5 How to Add Smooth Blending and Transition Effects Between Slides

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

6 ActiveICM

6.1 How to Embed in Microsoft PowerPoint 2003

6.2 How to Embed in Microsoft PowerPoint 2007

6.3 Embed in Web Browser

6.4 How to Use ActiveICM in PowerPoint

6.5 How to Change ActiveICM Component Properties

6.6 Advanced use of activeICM: Macros to direct visualisation changes

7 Movie Making

7.1 Movie Making Options

7.2 Screen-grabbing Movie

7.3 View-Defined Movie Making

8 Working with Sequences and Alignments

8.1 Load Sequence

8.2 Bioinfo Menu

8.3 Seqeunce Search and Align

8.4 Sequence Alignments

8.5 Alignment Editor

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 Proteins Superposition

10.2 Quick Superimpose

10.3 Superimpose by 3D

10.4 Superimpose Multiple Proteins

10.5 Arrange as Grid

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 Homology Menu and Modelling Tools

12.1 Homology Modeling Introduction

12.2 Getting Started

12.3 Build Model

12.4 Interactive Modeling

12.5 Display Loops

12.6 Loop Modeling

12.7 Regularization

12.8 Refine Side Chains

12.9 Making a disulfide bond.

13 3D Predict

13.1 Assign Helices and Strands

13.2 Protein Health

13.3 Local Flexibility

13.4 Protein-Protein Interface Prediction

13.5 Identfy Ligand Pockets

14 Molecular Mechanics

14.1  ICM Convert

14.2  Optimize H,His,Asn,Gln,Pro

14.3  Regularization

14.4  Impose Conformation

14.5  Edit Structure

14.6  MMFF

14.7  Minimize

14.8  Sample Loop

14.9  Generate Normal Mode Stack

14.10 Stack

14.11 GAMESS

14.12 Energy Terms

15 Cheminformatics

15.1  Reading Chemical Structures

15.2  Working with Chemical Spreadsheets.

15.3  Molecular Editor

15.4  How to extract a 2D sketch of a ligand in complex with a PDB strcture.

15.5  Saving Chemical Structures and Images

15.6  Export to Excel

15.7  IUPAC Chemical Nomenclature

15.8  Chemical Search

15.9  Pharmacophore Drawing and Searching

15.10 Find and Replace

15.11 Generating Chemical Fragments

15.12 Molcart

16 Chemistry Menu

16.1  Calculate Properties

16.2  Standardize Table

16.3  Annotate By Substructure

16.4  Build Prediction Model

16.5  Predict

16.6  Convert Smiles to 2D

16.7  Convert Structure to Smiles

16.8  2D Depiction

16.9  Convert to 3D

16.10 Generate 3D Conformers

16.11 Generate Tautomers

16.12 Convert to Racemic

16.13 Generate Stereoismers

16.14 Align/Color by 2D Scaffold

16.15 Cluster Set

16.16 Compare Two Sets

16.17 Merge Two Sets

16.18 Sort Table

16.19 Select Duplicates

16.20 Create/Modify Markush

16.21 Enumerate by Scaffold

16.22 R-Group Decomposition

16.23 Enumerate by Reaction

16.24 Superposition

17 Docking

17.1 Small Molecule Docking

17.2 Flexible Receptor Docking and Multiple Receptor Conformations

17.3 Template Docking

17.4 Virtual Ligand Screening

17.5 ICM X-Ray AutoFit - Automated Model Building into Density

17.6 Protein-Protein Docking

18 How To Use The Ligand Editor

18.1 Setup Ligand and Receptor

18.2 Ligand-Editor-Preferences

18.3 Pocket Display Options

18.4 Re-Dock and Minimize Ligand

18.5 Edit Ligand

18.6 Insert a linker

18.7 Find Best Replacement Group

18.8 Impose Restraint (tethers) To Ligand Atoms

19 Working with Tables

19.1 Standard ICM Tables

19.2 Molecular Tables

19.3 Plotting Table Data

19.4 Principal Component Analysis

19.5 Learn and Predict

19.6 Cluster

20 Working with Local Databases

20.1 How to make a local database.

20.2 Browse Database

20.3 Edit Database

20.4 Query Local Database

21 Frequently Asked Questions

21.1 FAQ Installation

21.2 FAQ Hardware

21.3 FAQ Graphics and Display

21.4 FAQ Structure

21.5 FAQ-Docking

21.6 FAQ-Cheminformatics

21.7 FAQ-Simulations

21.8 FAQ-Script

21.9 Troubleshooting

22 Tutorials

22.1  Graphical Display Tutorial: Molecule Representation, Coloring, Labeling and Annotation

22.2  Graphical Selections Tutorial

22.3  Generating Fully Interactive Slides for PowerPoint and the Web Tutorial

22.4  Working with PDB Structures

22.5  Sequence and Alignment Tutorial

22.6  Ligand Binding Pocket Analysis Examples

22.7  Homology Modeling and Structure Analysis Tools

22.8  Protein Preparation and Crystallographic Analysis Tutorial

22.9  Working with the Molecular Editor

22.10 Chemical Searching

22.11 How to Convert Chemicals from 2D to 3D

22.12 How to Work with the ICM 3D Ligand Editor

22.13 How to Superimpose Chemicals

22.14 How to Generate Plots and Histograms

22.15 How to Build and Apply QSAR Prediction Models

22.16 Docking Examples

22.17 Virtual Screening Examples

22.18 Docking a Markush Library

22.19 Multiple Receptor Conformation Ensemble Docking Example

22.20 Explicit Group Docking