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

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  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 Torsion Analysis

7.17 Calculate Torsion Free Strain

7.18 Enumerate Formal Charge States

7.19 Protonation States vs pH

7.20 Convert

7.21 Build Prediction Model

7.22 Predict

7.23 Generate 3D Conformers

7.24 Generate Tautomers

7.25 Generate Stereoisomers

7.26 Prodrug

7.27 Ligand Energetics

7.28 Cluster Set

7.29 PCA Analysis

7.30 Visualize Chemical Space

7.31 Compare Two Sets

7.32 Merge Two Sets

7.33 Select Duplicates

7.34 Multi Parameter Optimization

7.35 Combinatorial Chemistry

7.36 SAR Analysis

7.37 Chemical Superposition

7.38 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 Molecular Dynamics

9.1 Run Molecular Dynamics

9.2 Restraints

9.3 Membrane

9.4 MD of VLS Hitlist

10 MolScreen

10.1 Load Models and Run MolScreen

10.2 Results Table

10.3 Model Types

10.4 Custom Model Panel

10.5 Make Chemical Classification Model

10.6 Make APF Docking SAR Model

10.7 Predict Metabolic Oxidation

11 The 3D Fully Interactive Ligand Editor

11.1  Setup Ligand and Receptor

11.2  Ligand-Editor-Preferences

11.3  Display Options

11.4  Evaluate Ligand Score and Strain

11.5  Edit Ligand

11.6  Virtual Screen: Find Best Replacement Group

11.7  Multiple Position Group Scan

11.8  Bioisostere Scan

11.9  Dock or Minimize Ligand

11.10 Dock from Table

11.11 Fragment Linking Core Replacement

11.12 Impose Tethers or Distance Restraints

11.13 Defined Flexible Receptor Groups

11.14 Side Chain Refinement

11.15 Multiple Receptor Docking

11.16 Covalent Docking in the Ligand Editor

11.17 Dock to Atomic Property Fields

11.18 How to Save Ligand Receptor Complex as PDB

11.19 Export Docking Project.

11.20 Close and Clean Up Project

12 Working with Tables and Plots

12.1 Standard ICM Tables

12.2 Molecular Tables

12.3 Insert Interactive Objects into Table Cell

12.4 Plotting Table Data

12.5 Principal Component Analysis

12.6 Learn and Predict

12.7 Data Clustering

13 Working with Local Databases

13.1 How to make a local database.

13.2 Browse Database

13.3 Edit Database

13.4 Query Local Database

13.5 Eficient Storage for Ultra-Large Virtual Chemical Databases

14 ICM in KNIME

15 Tutorials

15.1 Graphics Tutorials

15.2 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial

15.3 Protein Structure Tutorials

15.4 Cheminformatics Tutorials

15.5 3D Ligand Editor Tutorial

15.6 Atomic Property Field Tutorials

15.7 Chemical FingerPrint QSAR Model Tutorial

15.8 3D QSAR Tutorial