Sep 13 2018 Feedback.
Contents
 
Help Videos
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



Sep 13 2018

Feedback.

Table of contents

Help Videos on YouTube
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
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
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
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
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)
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
Learn and Predict
8.1 Learn
8.2 Predict
8.3 Fingerprint Methods
8.4 3D QSAR
8.5 A Little Theory on Learning
MolScreen
9.1 Model Types
9.2 Brief Panel
9.3 Full Model Panel
9.4 Custom Model Panel
9.5 Results Table
9.6 Make Chemical Classification Model
9.7 Make APF Docking SAR Model
9.8 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
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

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