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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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