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%atoms = (
   A  => [ -1.115,  8.537,  7.075 ],
...
   L  => [ 1.152, 11.081, 23.082 ],
   M  => [ 2.200, 17.590, 18.424 ],
);

%helixes = (
  helix1 => { 
...
    M  => { x => 2.200, y => 17.590, z => 18.424 },
  },
);