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.