ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Apr 11 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
ICM molecular objects
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An ICM molecular object represents one or several molecules which can coexist in physical space, so that the energy of the molecular system can be calculated. For example, if you have two homologous molecules superimposed, multiple conformations of the same structure such as NMR structure determinations or alternative positions of a side chain, they must belong to different objects. The number of objects that may be loaded in ICM is limited only by the available computer memory. Objects may be of several types (see also: the Type ( os_ 2 ) function):
  • "ICM" - the only complete type which is good for everything including energy calculations
  • "X-Ray" - incomplete (stripped) object created by read pdb. The structure is determined by X-ray crystallography. Good for graphics and geometrical analysis
  • "NMR" - incomplete (stripped) object, structure determined from NMR data, similar to the "X-ray" type above.
  • "Model" - incomplete (stripped) object, theoretical model also similar to the "X-ray" type above.
  • "Ca-trace" - incomplete (stripped) object, only alpha-carbon atoms.
  • "Simplified" - simplified representation.

ICM-molecular objects are created from residues and molecules described in the ICM residue library. Its content (sequences and names of molecules) is specified in an ICM sequence file (see also IcmSequence function). An ICM-object can also be created from a non-ICM object (e.g. of X-Ray type) with the convert command.

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