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 Save an ICM Object

2.11 How to Save an an ICM Project File

2.12 How to Manage the GUI Windows

2.13 GUI Helpful Tips

2.14 Quick Start: Sequences and Alignments

2.15 Quick Start: Protein Structure

2.16 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 Labeling

5.6 Displaying Tethers

5.7 Displaying Distance Restraints

5.8 Superimpose

5.9 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

9.1 Surfaces

9.2 Meshes and Macroshape

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 Sequences

13.1 Load Sequence

13.2 Sequence Alignments

14 Bioinfo Menu

14.1  Residue Content

14.2  Predict Secondary Structure

14.3  Six Frame Translation

14.4  Set Sequence Type

14.5  Align Two Sequences

14.6  Sequence Structure Alignment

14.7  Align DNA vs Protein

14.8  Multiple Sequence Alignment

14.9  Link to Structure

14.10 Extraxt Sub-Alignment As Is

14.11 Cut Vertical Alignment Block

14.12 Reorder Sequences

14.13 Extract Unique Sequences

14.14 Search and Align

15 Tools Menu - Xray

15.1 Crystallographic Neighbor

15.2 Crystallographic Cell

15.3 Biomolecule Generator

15.4 Get Electron Density Map

15.5 Map's Original Cell

15.6 Contour Electron Density Map

15.7 Convert Xray Density to Grid

16 Tools Menu - 3D Predict

16.1 Assign Helices and Strands

16.2 Protein Health

16.3 Local Flexibility

16.4 Protein Interface by ODA

16.5 icmPocketFinder

17 Tools Menu - Analysis

17.1 RMSD

17.2 Contact Areas

17.3 Closed Cavities

17.4 Surface Area

17.5 Distance

17.6 Planar Angle

17.7 Dihedral Angle

17.8 Ramachandran Plot

18 Tools Menu - Superimpose

18.1 Display and Select Proteins for Superposition

18.2 Proteins by 3D

18.3 Multiple Proteins

18.4 Arrange as Grid

19 Homology Menu and Modelling Tools

19.1 Homology Modeling Introduction

19.2 Build Model

19.3 Display Loops

19.4 Loop Modeling

19.5 Regularization

19.6 Refine Side Chains

19.7 Making a disulfide bond.

20 Working with Chemistry Tools

20.1 Reading Chemical Structures

20.2 Working with Chemical Spreadsheets.

20.3 Molecular Editor

20.4 Saving Chemical Structures and Images

21 Chemistry Menu

21.1  Calculate Properties

21.2  Standardize Table

21.3  Build Prediction Model

21.4  Predict

21.5  Convert Smiles to 2D

21.6  Convert Structure to Smiles

21.7  2D Depiction

21.8  Convert to 3D

21.9  Generate 3D Conformers

21.10 Generate Tautomers

21.11 Convert to Racemic

21.12 Generate Stereoismers

21.13 Align/Color by 2D Scaffold

21.14 Cluster Set

21.15 Compare Two Sets

21.16 Merge Two Sets

21.17 Sort Table

21.18 Select Duplicates

21.19 Enumerate by Markush

21.20 R-Group Decomposition

21.21 Enumerate by Reaction

21.22 Superposition

21.23 Chemical Search

21.24 Pharmacophore Drawing and Searching

21.25 Find and Replace

21.26 Generating Chemical Fragments

21.27 Molcart

22 Docking

22.1 Small Molecule Docking

22.2 Flexible Receptor Docking and Multiple Receptor Conformations

22.3 Template Docking

22.4 Virtual Ligand Screening

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

22.6 Protein-Protein Docking

23 Making Molecular Animations, Slides, and Documents

23.1 Molecular Animations and Transitions

23.2 Making Molecular Slides

23.3 Making Molecular Documents

24 Movie Making

24.1 Movie Making Options

24.2 Screen-grabbing Movie

24.3 View-Defined Movie Making

25 Frequently Asked Questions

25.1 FAQ Installation

25.2 FAQ Hardware

25.3 FAQ Graphics and Display

25.4 FAQ Structure

25.5 FAQ-Docking

25.6 FAQ-Cheminformatics

25.7 FAQ-Simulations

25.8 FAQ-Script

25.9 Troubleshooting

26 Tutorial - Working with the Graphical Display

26.1 Getting Started

26.2 Making Graphical Selections

26.3 Making Sequence Selections in the ICM Workspace

26.4 Making a Spherical Selection.

26.5 Filtering a Selection.

26.6 Propogating a selection to all atoms in a residue.

26.7 Coloring and Molecule Representations

26.8 Labeling and Annotation

27 Tutorial - Molecular Documents

27.1 Making a Molecular Document

27.2 How to Incorporate Tranistion Effects Between Slides

28 Tutorial - Working with PDB Protein Structures

28.1 PDB Searching

28.2 Converting a PDB File into an ICM Object

28.3 PDB Preparation - Symmetry

28.4 PDB Preparation - Occupancy and B-Factors

29 Tutorial - Working with Sequences and Alignments

29.1 Pairwise Alignments

29.2 Sequence Drag and Drop and the Alignment Editor

29.3 Multiple Sequence Alignments

29.4 Boxing Shading and Annotating an Alignment

30 Tutorial - Ligand Binding Pocket Analysis Examples

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

30.2 Displaying the sequence conservation around the ligand binding site.

30.3 Displaying hydrogen bonds between a ligand and receptor.

31 Tutorial - Homology Modeling and Structure Analysis Tools

31.1 Homology Modeling

31.2 Making an amino acid mutation

31.3 Protein Health

31.4 Superimpose Structures

32 Tutorial - Crystallographic Analysis Tools

32.1 Crystallographic Symmetry

32.2 Biomolecule Generator

33 Tutorial - Working with Chemical Tables

33.1 Reading and Displaying Chemical Structures

33.2 Adding more information (Columns) to a Chemical Table

33.3 Creating a grid view with multiple columns.

33.4 Sorting a table column

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

33.6 Renaming a Column and Adding Data.

34 Tutorial - Working with the Molecular Editor

34.1 Draw Chemical

34.2 Edit Chemical

35 Tutorial - Chemical Searching

35.1 Chemical Similarity Searching

35.2 Advanced Chemical Similarity Searching

35.3 3D Pharmacophore Searching

35.4 2D Pharmacophore Searching

36 Tutorial - Docking and Virtual Ligand Screening

36.1 Re-Dock Biotin to the Streptavidin Receptor

36.2 Re-Dock an Inhibitor to Ricin Crystal Structure

36.3 Virtual Ligand Screening to Ricin Receptor

36.4 Virtual Ligand Screening to Cyclooxygenase

36.5 Docking a Markush Library

36.6 Multiple Receptor Conformation Ensemble Docking Example