FlipAtom - flip atoms for better superpositionSYNOPSIS
FlipAtom nameListDESCRIPTION
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
DATE
950922