ICM-Chemist User Guide v.3.7-3b

Table of contents

1 How To Guides and Videos

1.1 ICM-Browser How To Guide

1.2 ICM-Browser-Pro How To Guide

1.3 ActiveICM How To Guide - Create 3D Molecular Documents for the Web and PowerPoint

1.4 ICM-Chemist How To Guide

2 Getting Started

2.1 How to Use the Graphical Display

2.2 Making Selections

2.3 Menu Option Guide

2.4 Tab Guide

3 Working with Protein Structures

3.1 Searching the PDB

3.2 Converting PDB Files Into ICM Objects

3.3 How to Display the Ligand Binding Pocket Surface and Neighboring Residues.

3.4 How to Display Hydrogen Bonds

4 Molecular Graphics

4.1  Molecule Representation

4.2  Meshes - Surface - Grobs

4.3  Coloring

4.4  Lighting

4.5  Labeling and Annotation

4.6  Display Distances and Angles

4.7  Graphics Effects

4.8  Graphics Shortcuts

4.9  Molecule Move Buttons

4.10 Clipping Tools

4.11 Graphic Layers

4.12 Make High Quality Publication Images

5 Molecular Animations, Slides, and Documents

5.1 Molecular Animations and Transitions

5.2 Making 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

6 ActiveICM

6.1 How to Embed in Microsoft PowerPoint 2003

6.2 How to Embed in Microsoft PowerPoint 2007

6.3 How to Embed in MicroSoft PowerPoint 2010

6.4 Embed in Web Browser

6.5 How to Use ActiveICM in PowerPoint

6.6 How to Change ActiveICM Component Properties

6.7 Advanced use of activeICM: Macros to direct visualisation changes

6.8 Background Images

7 Movie Making

8 Protein Structure Analysis

8.1  Find Related Chains

8.2  Calculate RMSD

8.3  Contact Areas

8.4  Identify Closed Cavities

8.5  Surface Area

8.6  Measure Distances

8.7  Planar Angle

8.8  Dihedral Angle

8.9  Ramachandran Plot Interactive

8.10 Export Ramachandran Plot

9 Protein Superposition

9.1 Select Proteins for Superposition

9.2 Superimpose Button

9.3 Superimpose by 3D

9.4 Superimpose Multiple Proteins

9.5 Arrange as Grid

9.6 Superimpose Sites by Atomic Property Fields

10 Crystallographic Analysis

10.1  Crystallographic Neighbor

10.2  Crystallographic Cell

10.3  Biomolecule Generator

10.4  Get Electron Density Map

10.5  Map's Original Cell

10.6  Contour Electron Density Map

10.7  Convert Xray Density to Grid

10.8  Protein Health

10.9  Local Flexibility

10.10 Protein-Protein Interface Prediction

10.11 Identfy Ligand Pockets

11 Cheminformatics

11.1  Reading Chemical Structures

11.2  Working with Chemical Spreadsheets.

11.3  Molecular Editor

11.4  How to extract a 2D sketch of a ligand in complex with a PDB structure.

11.5  Saving Chemical Structures and Images

11.6  Export to Excel

11.7  IUPAC Chemical Nomenclature

11.8  Chemical Search

11.9  Pharmacophore Drawing and Searching

11.10 Find and Replace

11.11 Generating Chemical Fragments

11.12 Molcart

12 Chemistry Menu

12.1  Calculate Properties

12.2  Standardize Table

12.3  Annotate By Substructure

12.4  Align/Color by 2D Scaffold

12.5  Set Formal Charges

12.6  Convert

12.7  Predict

12.8  Generate Tautomers

12.9  Generate Stereoisomers

12.10 Ligand Energetics

12.11 Cluster Set

12.12 PCA Analysis

12.13 Compare Two Sets

12.14 Merge Two Sets

12.15 Select Duplicates

12.16 Combinatorial Chemistry

13 Working with Tables

13.1 Standard ICM Tables

13.2 Molecular Tables

13.3 Insert Interactive Objects into Table Cell

13.4 Plotting Table Data

13.5 Principal Component Analysis

13.6 Learn and Predict

13.7 Cluster

14 Working with Local Databases

14.1 How to make a local database.

14.2 Browse Database

14.3 Edit Database

14.4 Query Local Database

15 ICM in KNIME

16 Tutorials

16.1 Graphics Tutorials

16.2 Cheminformatics Tutorials