Mar 10 2017 Feedback.
Contents
 
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Cheminformatics
Learn and Predict
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
KNIME
Tutorials
 
Index

ICM-Chemist-Pro User Guide v.3.8

by Ruben Abagyan, Andrew Orry, Eugene Raush, and Maxim Totrov
Copyright © 2017



Mar 10 2017

Feedback.

Table of contents

Reference Guide
1.1 ICM-Browser Reference Guide
1.2 ICM-Browser-Pro Reference Guide
1.3 ActiveICM Reference Guide - Create 3D Molecular Documents for the Web and PowerPoint
1.4 ICM-Chemist Reference Guide
1.5 ICM-Chemist-Pro Reference Guide
1.6 Menu Option Guide
1.7 Tab Guide
Getting Started
2.1 The Basics of the Graphical User Interface
2.2 How to search and download Protein Structure, Sequences, and Chemicals
2.3 Create New Objects
2.4 Open and Read Files
2.5 Saving Files
2.6 Making Selections
2.7 Preferences
Protein Structure
3.1 Convert to ICM Object
3.2 Pocket Display
3.3 Crystallographic Analysis
3.4 Protein Superposition
3.5 Protein Structure Analysis
Molecular Graphics
4.1  Molecule Representation
4.2  Multi-Windows
4.3  Meshes - Surface - Grobs
4.4  Coloring
4.5  Lighting
4.6  3D Stereo
4.7  3D Printing
4.8  Labeling and Annotation
4.9  Display Distances and Angles
4.10 Graphics Effects
4.11 Graphics Shortcuts
4.12 Molecule Move Buttons
4.13 Clipping Tools
4.14 Graphic Layers
4.15 High Quality Publication Images
4.16 Movie Making
Slides & ActiveICM
5.1  Making Slides
5.2  Make a Movie from a Set of 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
5.7  ActiveICM
5.8  How to Embed in Microsoft PowerPoint 2003
5.9  How to Embed in Microsoft PowerPoint 2007
5.10 How to Embed in MicroSoft PowerPoint 2010
5.11 Embed in Web Browser
5.12 How to Use ActiveICM in PowerPoint
5.13 How to Change ActiveICM Component Properties
5.14 Advanced use of activeICM: Macros to direct visualisation changes
5.15 Background Images
5.16 ICM JavaScript (IcmJS)
Cheminformatics
6.1  Read Chemical Structures
6.2  Save Chemical Structures and Images
6.3  Working with Chemical Spreadsheets.
6.4  Molecular Editor
6.5  Chemical Search
6.6  2D Ligand Interaction Diagram
6.7  Convert Chemicals to 3D
6.8  Generating Chemical Fragments
6.9  Find Bioisostere
6.10 Molcart
6.11 Calculate Properties
6.12 Standardize Table
6.13 Annotate By Substructure
6.14 Align/Color by 2D Scaffold
6.15 Set Formal Charges
6.16 Enumerate Formal Charge States
6.17 Convert
6.18 Build Prediction Model
6.19 Predict
6.20 Generate 3D Conformers
6.21 Generate Tautomers
6.22 Generate Stereoisomers
6.23 Prodrug
6.24 Ligand Energetics
6.25 Cluster Set
6.26 PCA Analysis
6.27 Compare Two Sets
6.28 Merge Two Sets
6.29 Select Duplicates
6.30 Multi Parameter Optimization
6.31 Combinatorial Chemistry
6.32 SAR Analysis
6.33 Substructure Superposition
6.34 Atomic Property Field Superposition
6.35 APF Tools
Learn and Predict
7.1 Learn
7.2 Predict
7.3 Fingerprint Methods
7.4 3D QSAR
7.5 A Little Theory on Learning
MolScreen
8.1 Model Types
8.2 Brief Panel
8.3 Full Model Panel
8.4 Custom Model Panel
8.5 Results Table
8.6 Make Chemical Classification Model
8.7 Make APF Docking SAR Model
8.8 Predict Metabolic Oxidation
The 3D Fully Interactive Ligand Editor
9.1  Setup Ligand and Receptor
9.2  Ligand-Editor-Preferences
9.3  Display Options
9.4  Evaluate Ligand Score and Strain
9.5  Edit Ligand
9.6  Virtual Screen: Find Best Replacement Group
9.7  Multiple Position Group Scan
9.8  Dock or Minimize Ligand
9.9  Dock from Table
9.10 Fragment Linking
9.11 Impose Tethers or Distance Restraints
9.12 Defined Flexible Receptor Groups
9.13 Side Chain Refinement
9.14 Multiple Receptor Docking
9.15 Covalent Docking in the Ligand Editor
9.16 Dock to Atomic Property Fields
9.17 How to Save Ligand Receptor Complex as PDB
9.18 Export Docking Project.
9.19 Close and Clean Up Project
10 Working with Tables and Plots
10.1 Standard ICM Tables
10.2 Molecular Tables
10.3 Insert Interactive Objects into Table Cell
10.4 Plotting Table Data
10.5 Principal Component Analysis
10.6 Learn and Predict
10.7 Data Clustering
11 Working with Local Databases
11.1 How to make a local database.
11.2 Browse Database
11.3 Edit Database
11.4 Query Local Database
12 ICM in KNIME
13 Tutorials
13.1 Graphics Tutorials
13.2 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial
13.3 Protein Structure Tutorials
13.4 Cheminformatics Tutorials
13.5 3D Ligand Editor Tutorial
13.6 Atomic Property Field Tutorials
13.7 Chemical FingerPrint QSAR Model Tutorial
13.8 3D QSAR Tutorial

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