ICM Graphical User Interface Guide v.3.0

Table of contents

1 Introduction

1.1 ICM Specifications and Recomendations

1.2 Products and Features

1.3 Requesting an ICM license and Installation

2 Graphical User Interface Overview - RECOMMENDED READING FOR NEW ICM USERS

2.1  How to load a PDB Structure

2.2  How to Move a Structure in the Graphical Display

2.3  How to Make Selections

2.4  How to Change the Selection Level and Mode

2.5  How to Check What is Selected

2.6  How to use the ICM Workspace Panel

2.7  How to Display a Molecule

2.8  How to Change Protein Representation

2.9  How to Color

2.10 How to Display a Binding Pocket Surface

2.11 How to Save an ICM Object

2.12 How to Save an an ICM Project File

2.13 How to Manage the GUI Windows

2.14 GUI Helpful Tips

2.15 Quick Start: Sequences and Alignments

2.16 Quick Start: Protein Structure

2.17 Quick Start: Cheminformatics

3 File Menu

3.1  New

3.2  Open

3.3  Extract from ICB

3.4  Load

3.5  Save Project

3.6  Save Project As

3.7  Quick Image

3.8  Write Image

3.9  Preferences

3.10 Recent Files

3.11 Recent PDB Codes

3.12 Quit

4 Graphics Move Tools

4.1 Keyboard and Mouse Shortcuts

4.2 Move Buttons

5 Display Tab

5.1  Display and Undisplay Hydrogens

5.2  Structure Representation

5.3  Hydrogen Bonding

5.4  Coloring

5.5  Background Image

5.6  Labeling

5.7  Displaying Tethers

5.8  Displaying Distance Restraints

5.9  Superimpose

5.10 Display Clash

6 Light Tab

7 Labels Tab

7.1 Customized Label 2D or 3D

7.2 Displaying Distances

7.3 (Un)display Origin

8 PDB Search Tab

8.1 Searching the PDB

8.2 Finding a PDB Structure

8.3 Querying PDB by Keyword or PDB Code

8.4 Querying PDB by Sequence Pattern

8.5 Sensitive PDB Similarity Searches

8.6 Working with PDB Search Results

8.7 Converting PDB Files Into ICM Objects

9 Meshes Tab and 3D Objects

9.1 Surfaces

9.2 Meshes and Macroshape

9.3 Google 3D Objects (Sketchup)

9.4 Mesh Options.

10 View Menu and Tools

10.1  Undisplay All

10.2  Clear-Display-and-Planes

10.3  Selection Level

10.4  Selection Mode

10.5  Fog

10.6  Side-by-Side Stereo

10.7  Hardware Stereo

10.8  Full Screen

10.9  Perspective

10.10 Full Scene Antialias

10.11 High Quality

10.12 Easy Rotate

10.13 Shadows

10.14 Animate View

10.15 Drag Res Labels

10.16 Antialias Lines

10.17 Color Background

10.18 Save Viewpoint

10.19 Center

10.20 Macro Shape

10.21 Select by Purple 3D Box

10.22 Clipping Tools

10.23 Mesh Clipping

11 Making Selections

11.1 Graphical Selections

11.2 Workspace Selections

11.3 Selecting Neighbors

11.4 Alignment and Table Selections

11.5 Making Links

12 Working with Tables

12.1 Standard ICM Tables

12.2 Molecular Tables

12.3 Plotting Table Data

12.4 Principal Component Analysis

12.5 Learn and Predict

12.6 Cluster

13 Working with Local Databases

14 Working with Sequences

14.1 Load Sequence

14.2 Sequence Alignments

15 Bioinfo Menu

15.1  Residue Content

15.2  Predict Secondary Structure

15.3  Six Frame Translation

15.4  Set Sequence Type

15.5  Align Two Sequences

15.6  Sequence Structure Alignment

15.7  Align DNA vs Protein

15.8  Multiple Sequence Alignment

15.9  Link to Structure

15.10 Extraxt Sub-Alignment As Is

15.11 Cut Vertical Alignment Block

15.12 Reorder Sequences

15.13 Extract Unique Sequences

15.14 Search and Align

16 Tools Menu - Xray

16.1 Crystallographic Neighbor

16.2 Crystallographic Cell

16.3 Biomolecule Generator

16.4 Get Electron Density Map

16.5 Map's Original Cell

16.6 Contour Electron Density Map

16.7 Convert Xray Density to Grid

17 Tools Menu - 3D Predict

17.1 Assign Helices and Strands

17.2 Protein Health

17.3 Local Flexibility

17.4 Protein Interface by ODA

17.5 icmPocketFinder

18 Tools Menu - Analysis

18.1 RMSD

18.2 Contact Areas

18.3 Closed Cavities

18.4 Surface Area

18.5 Distance

18.6 Planar Angle

18.7 Dihedral Angle

18.8 Ramachandran Plot

19 Tools Menu - Superimpose

19.1 Display and Select Proteins for Superposition

19.2 Proteins by 3D

19.3 Multiple Proteins

19.4 Arrange as Grid

20 Homology Menu and Modelling Tools

20.1 Homology Modeling Introduction

20.2 Build Model

20.3 Display Loops

20.4 Loop Modeling

20.5 Regularization

20.6 Refine Side Chains

20.7 Making a disulfide bond.

21 Working with Chemistry Tools

21.1 Reading Chemical Structures

21.2 Working with Chemical Spreadsheets.

21.3 Molecular Editor

21.4 Saving Chemical Structures and Images

21.5 Export to Excel

21.6 IUPAC Chemical Nomenclature

22 Chemistry Menu

22.1  Calculate Properties

22.2  Standardize Table

22.3  Build Prediction Model

22.4  Predict

22.5  Convert Smiles to 2D

22.6  Convert Structure to Smiles

22.7  2D Depiction

22.8  Convert to 3D

22.9  Generate 3D Conformers

22.10 Generate Tautomers

22.11 Convert to Racemic

22.12 Generate Stereoismers

22.13 Align/Color by 2D Scaffold

22.14 Cluster Set

22.15 Compare Two Sets

22.16 Merge Two Sets

22.17 Sort Table

22.18 Select Duplicates

22.19 Enumerate by Markush

22.20 R-Group Decomposition

22.21 Enumerate by Reaction

22.22 Superposition

22.23 Chemical Search

22.24 Pharmacophore Drawing and Searching

22.25 Find and Replace

22.26 Generating Chemical Fragments

22.27 Molcart

23 Docking

23.1 Small Molecule Docking

23.2 Flexible Receptor Docking and Multiple Receptor Conformations

23.3 Template Docking

23.4 Virtual Ligand Screening

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

23.6 Protein-Protein Docking

24 How To Use The Ligand Editor

24.1 Setup Ligand and Receptor

24.2 Ligand-Editor-Preferences

24.3 Display Pocket - Property, H-Bond, and Energy

24.4 Re-Dock Ligand

24.5 Edit Ligand

24.6 Impose Restraint (tethers) To Ligand Atoms

25 Making Molecular Animations, Slides, and Documents

25.1 Molecular Animations and Transitions

25.2 Making Molecular Slides

25.3 Making Molecular Documents

26 ActiveICM

26.1 Embed in Microsoft PowerPoint

26.2 Embed Web Browser

27 Movie Making

27.1 Movie Making Options

27.2 Screen-grabbing Movie

27.3 View-Defined Movie Making

28 Frequently Asked Questions

28.1 FAQ Installation

28.2 FAQ Hardware

28.3 FAQ Graphics and Display

28.4 FAQ Structure

28.5 FAQ-Docking

28.6 FAQ-Cheminformatics

28.7 FAQ-Simulations

28.8 FAQ-Script

28.9 Troubleshooting

29 Tutorial - Working with the Graphical Display

29.1 Getting Started

29.2 Making Graphical Selections

29.3 Making Sequence Selections in the ICM Workspace

29.4 Making a Spherical Selection.

29.5 Filtering a Selection.

29.6 Propogating a selection to all atoms in a residue.

29.7 Coloring and Molecule Representations

29.8 Labeling and Annotation

30 Tutorial - Molecular Documents

30.1 Making a Molecular Document

30.2 How to Incorporate Tranistion Effects Between Slides

31 Tutorial - Working with PDB Protein Structures

31.1 PDB Searching

31.2 Converting a PDB File into an ICM Object

31.3 PDB Preparation - Symmetry

31.4 PDB Preparation - Occupancy and B-Factors

32 Tutorial - Working with Sequences and Alignments

32.1 Pairwise Alignments

32.2 Sequence Drag and Drop and the Alignment Editor

32.3 Multiple Sequence Alignments

32.4 Boxing Shading and Annotating an Alignment

33 Tutorial - Ligand Binding Pocket Analysis Examples

33.1 Displaying only the residues that surround the ligand binding pocket.

33.2 Displaying the sequence conservation around the ligand binding site.

33.3 Displaying hydrogen bonds between a ligand and receptor.

34 Tutorial - Homology Modeling and Structure Analysis Tools

34.1 Homology Modeling

34.2 Making an amino acid mutation

34.3 Protein Health

34.4 Superimpose Structures

35 Tutorial - Crystallographic Analysis Tools

35.1 Crystallographic Symmetry

35.2 Biomolecule Generator

36 Tutorial - Working with Chemical Tables

36.1 Reading and Displaying Chemical Structures

36.2 Adding more information (Columns) to a Chemical Table

36.3 Creating a grid view with multiple columns.

36.4 Sorting a table column

36.5 Filtering the table by the values contained within a column.

36.6 Renaming a Column and Adding Data.

37 Tutorial - Working with the Molecular Editor

37.1 Draw Chemical

37.2 Edit Chemical

38 Tutorial - Chemical Searching

38.1 Chemical Similarity Searching

38.2 Advanced Chemical Similarity Searching

38.3 3D Pharmacophore Searching

38.4 2D Pharmacophore Searching

39 Tutorial - Docking and Virtual Ligand Screening

39.1 Re-Dock Biotin to the Streptavidin Receptor

39.2 Re-Dock an Inhibitor to Ricin Crystal Structure

39.3 Virtual Ligand Screening to Ricin Receptor

39.4 Virtual Ligand Screening to Cyclooxygenase

39.5 Docking a Markush Library

39.6 Multiple Receptor Conformation Ensemble Docking Example