May 8 2008
Contents
 
Introduction
 ICM Specifications
 Products and Features
 License
Overview - RECOMMENDED READING FOR NEW ICM USERS
File Menu
Graphics Move Tools
Display Tab
Light Tab
Labels Tab
PDB Search Tab
Meshes Tab
View Menu
Selections
Tables
Sequences
Bioinfo Menu
Tools Menu - Xray
Tools Menu - 3D Predict
Tools Menu - Analysis
Tools Menu - Superimpose
Homology and Modelling
Working with Chemistry Tools
Chemsitry Menu
Docking
Animations, Slides, & Documents
Movie Making
Frequently Asked Questions
Tutorial - Graphical Display
Molecular Document
Tutorial - Working with PDB Protein Structures
Tutorial - Working with Sequence Alignments
Tutorial - Ligand Binding Pocket Analysis
Tutorial - Homology and Modeling Tools
Tutorial - Crystallographic Analysis Tools
Tutorial - Working with Chemical Tables
Tutorial - Working with the Molecular Editor
Tutorial - Chemical Searching
Tutorial - Docking and Virtual Ligand Screening
 
Index
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1 Introduction
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NOTE: If you are reading this manual in a printed book form then additions to the manual describing new updates and improvements to ICM are available online at www.molsoft.com or in PDF format from our FTP (ftp.molsoft.com) site.

Also in this chapter:

ICM Specifications and Recomendations

ICM Products and Features

Requesting an ICM License and Installation

The ICM Suite of Software provides an easy to use general environment for a biologist or chemist who is curious about protein structure. In just a few seconds you can browse hundreds of structures of interest, analyze and visualize sequences, alignments and binding sites. Also you can perform molecular modeling, fully-flexible ligand and receptor docking, virtual ligand screening, chemical similarity searching, chemical clustering and much more... This book describes how to use the program via the Graphical User Interface (GUI) without the knowledge of the commands and functions running through your terminal window. After reading this book you may read the full ICM Language Reference Manual (www.molsoft.com/man) for the dying breed of command line users and occasional programmers. This is a separate document which is provided with a full ICM distribution or can be obtained from Molsoft in a printed form.

ICM is constantly updated with new features and so it is always a good idea to keep an eye on the release notes.

Most of the things you will read in this manual are sort of natural or can be figured out by common sense and trial-and-error. However, if you like to read a "structured" description of the material, go ahead and read this.

Since this book is intended for basically anyone who is even remotely interested in molecules, some basic knowledge of biology and chemistry is implied. Do not try to find definitions of "atom" or "sequence" here, but most terms beyond that will be explained. A keyword search of this manual is available on the online version which is located at (www.molsoft.com/gui).

This book covers the graphical user interface only. For detailed information regarding ICM programming please consult the separate ICM language reference guide (www.molsoft.com/man).

If you want to have a more hands-on introduction to ICM you are always more than welcome to join us at one of our ICM workshops which are held periodically throughout the year (www.molsoft.com/training.html).


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