# CalcRmsd

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