ICM Graphical User Interface Guide v.3.6-1a

Table of contents

1 Introduction

2 How To?

2.1 How To: Graphical Display

2.2 How To: Sequences and Alignments

2.3 How to: Protein Structure

2.4 How To: Cheminformatics

2.5 How To: Chemical Spreadsheets

2.6 How To: - Molecular Documents (iSee File)

3 Menu Options

3.1  File Menu

3.2  Edit Menu

3.3  View Menu

3.4  Bioinfo Menu

3.5  Tools Menu - Xray

3.6  Tools Menu - 3D Predict

3.7  Tools Menu - Analysis

3.8  Tools Menu - Superimpose

3.9  Tools Menu - Table

3.10 Tools Menu - Chemical Search

3.11 Tools Menu - Molecular Editor

3.12 Homology Menu

3.13 Chemistry Menu

3.14 Docking Menu

3.15 MolMechanics Menu

3.16 Windows Menu

4 Graphics and View Tools

4.1 Change Representations

4.2 View Tools

4.3 Keyboard and Mouse Shortcuts

4.4 Move Buttons

4.5 Clipping Tools

4.6 Graphic Layers

5 Tabs

5.1 Display Tab

5.2 Light Tab

5.3 Labels Tab

5.4 PDB Search Tab

5.5 Meshes Tab

5.6 Movie Tab

6 Making Selections

6.1 Graphical Selections

6.2 Workspace Selections

6.3 Selecting Neighbors

6.4 Alignment and Table Selections

6.5 Making Links

7 Working with Tables

7.1 Standard ICM Tables

7.2 Molecular Tables

7.3 Plotting Table Data

7.4 Principal Component Analysis

7.5 Learn and Predict

7.6 Cluster

8 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

9 Working with Sequences

9.1 Load Sequence

9.2 Sequence Alignments

10 Homology Menu and Modelling Tools

10.1 Homology Modeling Introduction

10.2 Getting Started

10.3 Build Model

10.4 Interactive Modeling

10.5 Display Loops

10.6 Loop Modeling

10.7 Regularization

10.8 Refine Side Chains

10.9 Making a disulfide bond.

11 Working with Chemistry Tools

11.1 Reading Chemical Structures

11.2 Working with Chemical Spreadsheets.

11.3 Molecular Editor

11.4 Saving Chemical Structures and Images

11.5 Export to Excel

11.6 IUPAC Chemical Nomenclature

12 Chemistry Menu

12.1  Calculate Properties

12.2  Standardize Table

12.3  Build Prediction Model

12.4  Predict

12.5  Convert Smiles to 2D

12.6  Convert Structure to Smiles

12.7  2D Depiction

12.8  Convert to 3D

12.9  Generate 3D Conformers

12.10 Generate Tautomers

12.11 Convert to Racemic

12.12 Generate Stereoismers

12.13 Align/Color by 2D Scaffold

12.14 Cluster Set

12.15 Compare Two Sets

12.16 Merge Two Sets

12.17 Sort Table

12.18 Select Duplicates

12.19 Enumerate by Markush

12.20 R-Group Decomposition

12.21 Enumerate by Reaction

12.22 Superposition

12.23 Chemical Search

12.24 Pharmacophore Drawing and Searching

12.25 Find and Replace

12.26 Generating Chemical Fragments

12.27 Pharmacophore

12.28 Molcart

13 Docking

13.1 Small Molecule Docking

13.2 Flexible Receptor Docking and Multiple Receptor Conformations

13.3 Template Docking

13.4 Virtual Ligand Screening

13.5 ICM X-Ray AutoFit - Automated Model Building into Density

13.6 Protein-Protein Docking

14 How To Use The Ligand Editor

14.1 Setup Ligand and Receptor

14.2 Ligand-Editor-Preferences

14.3 Pocket Display Options

14.4 Re-Dock and Minimize Ligand

14.5 Edit Ligand

14.6 Insert a linker

14.7 Find Best Replacement Group

14.8 Impose Restraint (tethers) To Ligand Atoms

15 Making Molecular Animations, Slides, and Documents

15.1 Molecular Animations and Transitions

15.2 Making Molecular Slides

15.3 Making Molecular Documents

16 ActiveICM

16.1 Embed in Microsoft PowerPoint 2003

16.2 Embed in Microsoft PowerPoint 2007

16.3 Embed in Web Browser

16.4 Using activeICM during a presentation

16.5 Advanced use of activeICM: Macros to direct visualisation changes

17 Movie Making

17.1 Movie Making Options

17.2 Screen-grabbing Movie

17.3 View-Defined Movie Making

18 Frequently Asked Questions

18.1 FAQ Installation

18.2 FAQ Hardware

18.3 FAQ Graphics and Display

18.4 FAQ Structure

18.5 FAQ-Docking

18.6 FAQ-Cheminformatics

18.7 FAQ-Simulations

18.8 FAQ-Script

18.9 Troubleshooting

19 Tutorials

19.1  Working with the Graphical Display

19.2  Working with PDB Structures

19.3  Working with Sequences and Alignments

19.4  Ligand Binding Pocket Analysis Examples

19.5  Homology Modeling and Structure Analysis Tools

19.6  Crystallographic Analysis Tools

19.7  Working with the Molecular Editor

19.8  Chemical Searching

19.9  Docking Examples

19.10 Virtual Screening Examples

19.11 Docking a Markush Library

19.12 Multiple Receptor Conformation Ensemble Docking Example