ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Jan 4 2018

Contents
 
Introduction
Reference Guide
 ICM options
 Editing
 Graph.Controls
 Alignment Editor
 Constants
 Subsets
 Molecules
 Selections
 Fingerprints
 Regexp
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Arithmetics
 Flow control
 MolObjects
 Energy Terms
 Integers
 Reals
 Logicals
 Strings
 Preferences
 Tables
 Other
 Chemical
 Smiles
 Soap
 Gui programming
 Commands
 Functions
 Icm shell functions
 Macros
 Files
Command Line User's Guide
References
Glossary
 
Index
PrevICM Language Reference
Molecule intro
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Molecules are the main inhabitants of the ICM shell. The shell can contain many objects, each of which can be a soup (this expression belongs to my friend Gert Vriend) of separate molecules. Molecules, in turn contain residues and atoms. ICM can handle both raw objects, as they come from a PDB file or a mol-file, and a fully prepared for molecular modeling "ICM"-objects.


The non-ICM objects can be visualized, but they need to be converted into ICM-objects to perform the most interesting modeling operations. To specify the subsets of objects, molecules, residues, atoms and internal variables, you need to learn the language of molecular selections.
A quick preview of the selection language, using the picture above as an example:
 
 display a_2. cpk           # object selection (the second object) 
 display a_1.1 ribbon green # molecule 1 from object 1 
 display a_1.2/his xstick   # residue his12 shown as balls and sticks 
 color   a_/1.2/12/n* xstick blue  # atoms: color nitrogens in blue  

For an in-depth description of selections, read the next section.

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Selections

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