ICM-Pro User Guide v.3.7-2a

by Ruben Abagyan, Andrew Orry, Eugene Raush, and Maxim Totrov
Copyright © 2010


Jun 23 2011
Feedback.

Table of contents

Introduction
How To Guides and Videos
2.1 ICM-Browser How To Guide
2.2 ICM-Browser-Pro How To Guide
2.3 ActiveICM How To Guide - Create 3D Molecular Documents for the Web and PowerPoint
2.4 ICM-Chemist How To Guide
2.5 ICM-Chemist-Pro How To Guide
Getting Started
3.1 How to Use the Graphical Display
3.2 Making Selections
3.3 How to Work With Sequences and Alignments
3.4 Menu Option Guide
3.5 Tab Guide
Working with Protein Structures
4.1 Searching the PDB
4.2 Converting PDB Files Into ICM Objects
4.3 How to Display the Ligand Binding Pocket Surface and Neighboring Residues.
4.4 How to Display Hydrogen Bonds
Molecular Graphics
5.1  Molecule Representation
5.2  Meshes - Surface - Grobs
5.3  Coloring
5.4  Lighting
5.5  Labeling and Annotation
5.6  Display Distances and Angles
5.7  Graphics Effects
5.8  Graphics Shortcuts
5.9  Molecule Move Buttons
5.10 Clipping Tools
5.11 Graphic Layers
5.12 Make High Quality Publication Images
Molecular Animations, Slides, and Documents
6.1 Molecular Animations and Transitions
6.2 Making Slides
6.3 How to View and Navigate Slides
6.4 How to Edit Slides
6.5 How to Add Smooth Blending and Transition Effects Between Slides
6.6 How to Make Molecular Documents - Link HTML Text to Slides
ActiveICM
7.1 How to Embed in Microsoft PowerPoint 2003
7.2 How to Embed in Microsoft PowerPoint 2007
7.3 Embed in Web Browser
7.4 How to Use ActiveICM in PowerPoint
7.5 How to Change ActiveICM Component Properties
7.6 Advanced use of activeICM: Macros to direct visualisation changes
7.7 Background Images
Movie Making
8.1 Screen-grabbing Movie
8.2 View-Defined Movie Making
Working with Sequences and Alignments
9.1 Load Sequence
9.2 Bioinfo Menu
9.3 Sequence Search and Align
9.4 Sequence Alignments
9.5 Alignment Editor
10 Protein Structure Analysis
10.1  Find Related Chains
10.2  Calculate RMSD
10.3  Contact Areas
10.4  Identify Closed Cavities
10.5  Surface Area
10.6  Measure Distances
10.7  Planar Angle
10.8  Dihedral Angle
10.9  Ramachandran Plot Interactive
10.10 Export Ramachandran Plot
11 Protein Superposition
11.1 Select Proteins for Superposition
11.2 Superimpose Button
11.3 Superimpose by 3D
11.4 Superimpose Multiple Proteins
11.5 Arrange as Grid
12 Crystallographic Analysis
12.1 Crystallographic Neighbor
12.2 Crystallographic Cell
12.3 Biomolecule Generator
12.4 Get Electron Density Map
12.5 Map's Original Cell
12.6 Contour Electron Density Map
12.7 Convert Xray Density to Grid
13 Homology Menu and Modelling Tools
13.1 Homology Modeling Introduction
13.2 Getting Started
13.3 Build Model
13.4 Interactive Modeling
13.5 Display Loops
13.6 Loop Modeling
13.7 Regularization
13.8 Refine Side Chains
13.9 Making a disulfide bond.
14 3D Predict
14.1 Assign Helices and Strands
14.2 Protein Health
14.3 Local Flexibility
14.4 Protein-Protein Interface Prediction
14.5 Identfy Ligand Pockets
15 Molecular Mechanics
15.1  ICM Convert
15.2  Optimize H,His,Asn,Gln,Pro
15.3  Regularization
15.4  Impose Conformation
15.5  Edit Structure
15.6  MMFF
15.7  Minimize
15.8  Sample Loop
15.9  Generate Normal Mode Stack
15.10 Stack
15.11 GAMESS
15.12 Energy Terms
16 Cheminformatics
16.1  Reading Chemical Structures
16.2  Working with Chemical Spreadsheets.
16.3  Molecular Editor
16.4  How to extract a 2D sketch of a ligand in complex with a PDB strcture.
16.5  Convert Chemicals to 3D
16.6  Saving Chemical Structures and Images
16.7  Export to Excel
16.8  IUPAC Chemical Nomenclature
16.9  Chemical Search
16.10 Pharmacophore Drawing and Searching
16.11 Find and Replace
16.12 Generating Chemical Fragments
16.13 Molcart
17 Chemistry Menu
17.1  Calculate Properties
17.2  Standardize Table
17.3  Annotate By Substructure
17.4  Align/Color by 2D Scaffold
17.5  Set Formal Charges
17.6  Convert
17.7  Build Prediction Model
17.8  Predict
17.9  Generate 3D Conformers
17.10 Generate Tautomers
17.11 Generate Stereoismers
17.12 Cluster Set
17.13 PCA Analysis
17.14 Compare Two Sets
17.15 Merge Two Sets
17.16 Select Duplicates
17.17 Combinatorial Chemistry
17.18 Chemical Superposition
18 Docking
18.1 Small Molecule Docking
18.2 Flexible Receptor Docking and Multiple Receptor Conformations
18.3 Template Docking
18.4 Virtual Ligand Screening
18.5 ICM X-Ray AutoFit - Automated Model Building into Density
18.6 Protein-Protein Docking
19 How To Use The Ligand Editor
19.1 Setup Ligand and Receptor
19.2 Ligand-Editor-Preferences
19.3 Pocket Display Options
19.4 Re-Dock and Minimize Ligand
19.5 Edit Ligand
19.6 Insert a linker
19.7 Find Best Replacement Group
19.8 Impose Restraint (tethers) To Ligand Atoms
20 Working with Tables
20.1 Standard ICM Tables
20.2 Molecular Tables
20.3 Insert Interactive Objects into Table Cell
20.4 Plotting Table Data
20.5 Principal Component Analysis
20.6 Learn and Predict
20.7 Cluster
21 Working with Local Databases
21.1 How to make a local database.
21.2 Browse Database
21.3 Edit Database
21.4 Query Local Database
22 Tutorials
22.1 Graphics Tutorials
22.2 Sequence and Alignment Tutorials
22.3 Protein Structure Tutorials
22.4 Homology Modeling Tutorials
22.5 Cheminformatics Tutorials
22.6 How to Work with the ICM 3D Ligand Editor
22.7 Ligand Docking Tutorials
22.8 Virtual Ligand Screening Tutorials
22.9 Induced Fit (Flexibility) Docking Tutorials
23 Frequently Asked Questions
23.1  FAQ Installation
23.2  FAQ Hardware
23.3  FAQ Graphics and Display
23.4  FAQ ActiveICM
23.5  FAQ Structure
23.6  FAQ-Docking
23.7  FAQ-Cheminformatics
23.8  FAQ-Simulations
23.9  FAQ-Script
23.10 Troubleshooting