Aug 11 2015 Feedback.
Contents
 
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Tutorials
 
Index

ICM-Bio User Guide v.3.8

by Ruben Abagyan, Andrew Orry, Eugene Raush, and Maxim Totrov
Copyright © 2015



Aug 11 2015

Feedback.

Table of contents

Reference Guide
1.1 ICM-Browser Reference Guide
1.2 ICM-Browser-Pro Reference Guide
1.3 ActiveICM Reference Guide - Create 3D Molecular Documents for the Web and PowerPoint
1.4 ICM-Chemist Reference Guide
1.5 Menu Option Guide
1.6 Tab Guide
Getting Started
2.1 The Basics of the Graphical User Interface
2.2 How to search and download Protein Structure, Sequences, and Chemicals
2.3 Create New Objects
2.4 Open and Read Files
2.5 Saving Files
2.6 Making Selections
2.7 Preferences
Protein Structure
3.1 Convert to ICM Object
3.2 Pocket Display
3.3 Crystallographic Analysis
3.4 Protein Superposition
3.5 Protein Structure Analysis
Molecular Graphics
4.1  Molecule Representation
4.2  Meshes - Surface - Grobs
4.3  Coloring
4.4  Lighting
4.5  3D Stereo
4.6  3D Printing
4.7  Labeling and Annotation
4.8  Display Distances and Angles
4.9  Graphics Effects
4.10 Graphics Shortcuts
4.11 Molecule Move Buttons
4.12 Clipping Tools
4.13 Graphic Layers
4.14 High Quality Publication Images
4.15 Movie Making
Slides & ActiveICM
5.1  Making Slides
5.2  Make a Movie from a Set of 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
5.7  ActiveICM
5.8  How to Embed in Microsoft PowerPoint 2003
5.9  How to Embed in Microsoft PowerPoint 2007
5.10 How to Embed in MicroSoft PowerPoint 2010
5.11 Embed in Web Browser
5.12 How to Use ActiveICM in PowerPoint
5.13 How to Change ActiveICM Component Properties
5.14 Advanced use of activeICM: Macros to direct visualisation changes
5.15 Background Images
Working with Sequences and Alignments
6.1 Read and Save Sequences
6.2 Sequence Secondary Structure
6.3 Bioinfo Menu
6.4 BLAST Search
6.5 Sequence Alignments
6.6 Alignment Editor
Tutorials
7.1 Graphics Tutorials
7.2 Creating Fully Interactive Slides for PowerPoint and the Web Tutorial
7.3 Protein Structure Tutorials
7.4 Sequence and Alignment Tutorials

Copyright© 1989-2015, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.