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
