I try to model an heterodimer using this alignment
If it's a heterodimer, why are you imposing symmetry restraints? The two
subunits won't be the same.
each time it gives me this error message
define__595E> Number of selected atoms in sets 2 & 3 is not the
same: 121 128
You can't make two differently-sized sets of atoms symmetric.
Can you tell me please what's wrong in my alignment file
There's nothing wrong with your alignment file. But remove the symmetry
restraint from your Python script (in this case, use the automodel class
rather than MyModel).