NAME
     CalcRmsd - calculate RMSDs and displacements

SYNOPSIS
     CalcRmsd ( fit_pairs | as_is ) region
	 name name nameList name nameList nameList

DESCRIPTION
     Calculate RMSDs and displacements of all selected
     molecules. The first argument selects whether each
     pair of molecules is superimposed before calculating
     the RMSD, or whether the current orientation is
     used. This can be useful to calculate RMSDs of
     structures already overlaid with the Fit command.

     The second arguments selects the residue range
     used for superposition when calculating global
     RMSDs and global displacements.

     The third argument selects the name of the first
     property that is used for superposition. The user
     can either give a property defined with DefProp or
     one of the predefined properties. The RMSD values
     will be printed in the upper right part of the
     matrix. This property is also used for the
     superpositions when calculating displacements.

     The forth argument selects the name of the second
     property that is used for superposition. The RMSD
     values will be printed in the lower left part of
     the matrix.

     The fifth argument is a space separated list of
     property names. It defines the groups of molecules
     that are compared. All the molecules of a group
     must be given a common property with DefPropMol
     (e. g. g1 and g2), and the list of these properties
     must be given here.

     The sixth argument is the name of a property of the
     molecule that is used as reference for displacements
     and local RMSDs, typically the mean structure. If no
     name is given, average pairwise values will be
     calculated.

     The seventh argument is a space separated list of
     property names. The global displacements will be
     calculated for all the given properties. The
     property used for the superposition is always
     the one given as third argument.

     The eighth argument is a space separated list of
     property names. The local RMSDs will be calculated
     for all the given properties. The local RMSD of a
     residue is calculated by superimposing 3 residues
     centered at the given residue, using the property
     given as third argument, and calculating the RMSD
     of all 3 residue.

     The ninth argument is a space separated list of
     property names. The local displacements will be
     calculated for all the given properties. The local
     displacement of a residue is calculated by
     superimposing 3 residues centered at the given
     residue, using the property given as third argument,
     and calculating the RMSD of the middle residue.

     This command supports groups.

EXAMPLE
     CalcRmsd fit_pairs '5..32,37..55' 'bb' 'heavy' ''
	 'bb heavy heavysc' '' 'bb heavy'

SEE ALSO
     SelectMol, DefPropMol, DefPropAtom, Group, Fit

DATE
     960317
