ICM-Chemist-Pro 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 ICM-Chemist-Pro Reference Guide

2.6 Menu Option Guide

2.7 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 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  Convert Chemicals to 3D

7.8  Generating Chemical Fragments

7.9  Find Bioisostere

7.10 Molcart

7.11 Calculate Properties

7.12 Standardize Table

7.13 Annotate By Substructure

7.14 Align/Color by 2D Scaffold

7.15 Set Formal Charges

7.16 Enumerate Formal Charge States

7.17 Convert

7.18 Build Prediction Model

7.19 Predict

7.20 Generate 3D Conformers

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

7.34 Substructure Superposition

7.35 Atomic Property Field Superposition

7.36 APF Tools

8 Learn and Predict

8.1 Learn

8.2 Predict

8.3 Fingerprint Methods

8.4 3D QSAR

8.5 A Little Theory on Learning

9 MolScreen

9.1 Load Models and Run MolScreen

9.2 Results Table

9.3 Model Types

9.4 Custom Model Panel

9.5 Make Chemical Classification Model

9.6 Make APF Docking SAR Model

9.7 Predict Metabolic Oxidation

10 The 3D Fully Interactive Ligand Editor

10.1  Setup Ligand and Receptor

10.2  Ligand-Editor-Preferences

10.3  Display Options

10.4  Evaluate Ligand Score and Strain

10.5  Edit Ligand

10.6  Virtual Screen: Find Best Replacement Group

10.7  Multiple Position Group Scan

10.8  Bioisostere Scan

10.9  Dock or Minimize Ligand

10.10 Dock from Table

10.11 Fragment Linking Core Replacement

10.12 Impose Tethers or Distance Restraints

10.13 Docking Templates

10.14 Defined Flexible Receptor Groups

10.15 Side Chain Refinement

10.16 Multiple Receptor Docking

10.17 Covalent Docking in the Ligand Editor

10.18 Dock to Atomic Property Fields

10.19 How to Save Ligand Receptor Complex as PDB

10.20 Export Docking Project.

10.21 Close and Clean Up Project

11 Working with Tables and Plots

11.1 Standard ICM Tables

11.2 Molecular Tables

11.3 Insert Interactive Objects into Table Cell

11.4 Plotting Table Data

11.5 Principal Component Analysis

11.6 Learn and Predict

11.7 Data Clustering

12 Working with Local Databases

12.1 How to make a local database.

12.2 Browse Database

12.3 Edit Database

12.4 Query Local Database

13 ICM in KNIME

14 Tutorials

14.1 Graphics Tutorials

14.2 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial

14.3 Protein Structure Tutorials

14.4 Cheminformatics Tutorials

14.5 3D Ligand Editor Tutorial

14.6 Atomic Property Field Tutorials

14.7 Chemical FingerPrint QSAR Model Tutorial

14.8 3D QSAR Tutorial