// Creating RNAs first

/*
molecule m1, m2 ;

m1 = fd_helix( "arna", "uuuu", "rna" );
putpdb( "rna_1.pdb", m1);

m2 = fd_helix( "arna", "auga", "rna" );
putpdb( "rna_2.pdb", m2);
*/

// now aligning around the origin and standard frame

molecule m;

// reading PDBs and aligning

m = getpdb("rna_1.pdb");
setframe( 2, m, // aligning U4 from m1
":4,U3:C6",
":4,U3:C5", ":4,U3:N1",
":4,U3:C6", ":4,U3:N3" );
alignframe( m, NULL );
putpdb( "std_m1.pdb", m );

m = getpdb("rna_2.pdb");
setframe( 2, m, // aligning A1 from m2
":1,A5:C4",
":1,A5:C5", ":1,A5:N3",
":1,A5:C4", ":1,A5:N1" );
alignframe( m, NULL );
putpdb( "std_m2.pdb", m );