ICM-Chemist User Guide v.3.9

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

4.6 3D Similarity PDB Search

4.7 Scan Pockets by 3D Pharmacophore

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 Cheminformatics

7.1  Read Chemical Structures

7.2  Save Chemical Structures and Images

7.3  Working with Chemical Spreadsheets.

7.4  Molecular Editor

7.5  Chemical Search

7.6  2D Ligand Interaction Diagram

7.7  Generating Chemical Fragments

7.8  Find Bioisostere

7.9  Molcart

7.10 Calculate Properties

7.11 Standardize Table

7.12 Annotate By Substructure

7.13 Align/Color by 2D Scaffold

7.14 Set Formal Charges

7.15 Torsion Analysis

7.16 Calculate Torsion Free Strain

7.17 Enumerate Formal Charge States

7.18 Protonation States vs pH

7.19 Convert

7.20 Predict

7.21 Generate Tautomers

7.22 Generate Stereoisomers

7.23 Prodrug

7.24 Ligand Energetics

7.25 Cluster Set

7.26 PCA Analysis

7.27 Visualize Chemical Space

7.28 Compare Two Sets

7.29 Merge Two Sets

7.30 Select Duplicates

7.31 Multi Parameter Optimization

7.32 Combinatorial Chemistry

7.33 SAR Analysis

8 Molecular Dynamics

8.1 Run Molecular Dynamics

8.2 Restraints

8.3 Membrane

8.4 MD of VLS Hitlist

9 Working with Tables and Plots

9.1 Standard ICM Tables

9.2 Molecular Tables

9.3 Insert Interactive Objects into Table Cell

9.4 Plotting Table Data

9.5 Principal Component Analysis

9.6 Learn and Predict

9.7 Data Clustering

10 Working with Local Databases

10.1 How to make a local database.

10.2 Browse Database

10.3 Edit Database

10.4 Query Local Database

10.5 Eficient Storage for Ultra-Large Virtual Chemical Databases

11 Tutorials

11.1 Graphics Tutorials

11.2 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial

11.3 Protein Structure Tutorials

11.4 Cheminformatics Tutorials