please let me know the main deference between these two python scripts.
I suppose the deference is *this*:
the first one do the comparative modeling with the base of template for
all residues,
but the second one, do the same except for residues 197 - 198.
Yes, that's right.
But I see a main deference between the results (output structures)
are the applied methods of these two script are the same or not?
Of course the output structures will be different, because you're
optimizing a different set of residues. But the method used is the same
in both cases.