Jul 1 2004
Contents
 
Introduction
Reference Guide
User's guide
References
Glossary
 
Index
Table of contents
1 Introduction
1.1 Release notes
1.2 Brief history of ICM
1.3 ICM distribution and support
1.4 What can you do with ICM? (a program overview)
1.5 Notational conventions
1.6 Common abbreviations
1.7 Getting started
2 Reference Guide
2.1  ICM command line options
2.2  Command line editing
2.3  Graphics controls
2.4  Editing pairwise sequence-structure alignments
2.5  Constants
2.6  Subsets and index expressions
2.7  Molecule intro
2.8  Selections
2.9  Arithmetics
2.10 Flow control
2.11 ICM molecular objects
2.12 Energy and Penalty Terms
2.13 Integer shell parameters.
2.14 Real shell variables
2.15 Logical variables
2.16 String variables
2.17 Preferences
2.18 Tables (structures)
2.19 Other shell variables
2.20 Commands
2.21 Functions
2.22 Macros
2.23 Files
3 User's guide
3.1  ICM-shell
3.2  ICM graphics
3.3  Structure analysis
3.4  Sequence, searches and alignments
3.5  Energetics and electrostatics
3.6  Manipulations with molecules
3.7  Animation
3.8  Transformations and symmetry
3.9  Maps and factors
3.10 How to plot
3.11 How-to: Docking and Virtual Ligand Screening
3.12 Example scripts
4 References
4.1 General literature references
4.2 The main description of the ICM method
4.3 ICM algorithms
4.4 ICM applications
4.5 Credits
5 Glossary
5.1 A
5.2 B
5.3 C
5.4 D
5.5 E-H
5.6 S
5.7 T
5.8 U-Z

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