ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Jun 5 2024

Reference Guide
 ICM options
 Alignment Editor
 Cgi programming with icm
 Xml drugbank example
 Tree cluster
 Flow control
 Energy Terms
 Chemical Functions
 Gui programming
 Icm shell functions
Command Line User's Guide
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Molecule intro

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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