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The following script will aline two molecules.

 set mask1 [atomselect 4 "protein and backbone and resid 17 80 to 140 155 to 160 and noh" frame 1 ]
 set mask2 [atomselect 8 "protein and backbone and resid 702 765 to 825 840 to 845 and noh" frame 1 ]
 set mask3 [atomselect 8 "all" frame 1]
 set trans_mat [measure fit $mask2 $mask1]
 $mask3 move $trans_mat

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