# Fit

NAME

    Fit - calculate structure superpositions

SYNOPSIS

    Fit ( to_axes | to_first | circular | to_mean )
        nameList

DESCRIPTION

Calculate a superposition of all selected molecules, using the selected atoms (or the atoms with properties given by the second argument, see below). The number of selected atoms of all selected molecules must be the same, otherwise an error message is issued.

If the option 'to_axes' is selected, the principal axes of the structures are aligned to the axes of the coordinate system. This is useful for obtaining a standard orientation.

If the option 'to_first' is selected, the RMSD of each structure to the first structure is minimized separately.

If the option 'circular' is selected, the sum of the RMSDs from the first to the second, from the second to the third, ... and from the last to the first structure is minimized.

If the option 'to_mean' is selected, the sum of all RMSDs to the resulting mean structure is minimized.

The options 'circular' and 'to_mean' use a less efficient algorithm than 'to_first', they can take very long to calculate. Their use is therefore generally not recommended. They can help in rare cases where the algorithm used in 'to_first' is numerically unstable.

At least one molecule has to be selected for 'to_axes', at least two for all other options.

For only two selected molecules, all algorithms give the same result.

The RMSD to the mean averaged over all molecules for the selected atoms after the fit is printed on the status line.

The optional second argument gives a list of properties of atoms to be fitted, where the default is just all selected atoms. If several properties are given, the corresponding atoms are fitted in this order. This is useful when superimposing different molecules, and the fragments to be superimposed are not in the same order in all molecules. E. g. for superimposing fragments of two molecules like this:

        mol 1      mol 2
        10-20 <--> 15-25
        30-40 <--> 55-65
        50-60 <--> 35-45

Just selecting all these atoms would take all fragments in ascending order, making the following superposition:

        mol 1      mol 2
        10-20 <--> 15-25
        30-40 <--> 35-45
        50-60 <--> 55-65

For getting the desired result:

        DefPropAtom 'fragm1' '(#1:10-20 #2:15-25) & bb'
        DefPropAtom 'fragm2' '(#1:30-40 #2:55-65) & bb'
        DefPropAtom 'fragm3' '(#1:50-60 #2:35-45) & bb'
        Fit to_first 'fragm1 fragm2 fragm3'

This command supports groups.

EXAMPLE

    Fit to_first 'selected'

SEE ALSO

`SelectAtom`, `Group`, `DialMol`

DATE

961217