Mar 10 2017 Feedback.
Contents
 
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Cheminformatics
Tables and Plots
Local Databases
Tutorials
 
Index

ICM-Chemist 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 Menu Option Guide
1.6 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  Generating Chemical Fragments
6.8  Find Bioisostere
6.9  Molcart
6.10 Calculate Properties
6.11 Standardize Table
6.12 Annotate By Substructure
6.13 Align/Color by 2D Scaffold
6.14 Set Formal Charges
6.15 Enumerate Formal Charge States
6.16 Convert
6.17 Predict
6.18 Generate Tautomers
6.19 Generate Stereoisomers
6.20 Prodrug
6.21 Ligand Energetics
6.22 Cluster Set
6.23 PCA Analysis
6.24 Compare Two Sets
6.25 Merge Two Sets
6.26 Select Duplicates
6.27 Multi Parameter Optimization
6.28 Combinatorial Chemistry
6.29 SAR Analysis
Working with Tables and Plots
7.1 Standard ICM Tables
7.2 Molecular Tables
7.3 Insert Interactive Objects into Table Cell
7.4 Plotting Table Data
7.5 Principal Component Analysis
7.6 Learn and Predict
7.7 Data Clustering
Working with Local Databases
8.1 How to make a local database.
8.2 Browse Database
8.3 Edit Database
8.4 Query Local Database
Tutorials
9.1 Graphics Tutorials
9.2 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial
9.3 Protein Structure Tutorials
9.4 Cheminformatics Tutorials

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