NAME
     FlipAtom - flip atoms for better superposition

SYNOPSIS
     FlipAtom nameList

DESCRIPTION
     Exchanges sets of atom names in all selected
     residues if that leads to a better superposition to
     the first structure. The sets of atoms that can
     be exchanged is listed in the file:

	 $MOLMOLHOME/setup/FlipAtoms

     The specifications in this file list atoms that
     are part of one potential exchange operation on one
     line. Each set of (typically 2 or 3) atoms that will
     be permuted by this operation is inside a pair of
     parentheses.

     The atoms that can be exchanged are normally the
     atoms of rings that do not have a fixed orientation
     in an NMR structure (PHE, TYR), and the protons of
     methyl groups.

     This command is typcially used before calculating
     mean structures, or RMSDs that involve side chains.

     The command will make a report listing the atoms
     that were exchanged.

EXAMPLE
     FlipAtom "PHE TYR"

SEE ALSO
     PathNames, MeanMol, CalcRmsd

DATE
     950922
