I want Modeller to fit generated models by dope_loopmodel class.
But only structures derived from the same IL000* file are superimposed
to it. Also templates are aligned, but not to generated models.
Yes, the loopmodel class does exactly what you describe - it fits each
loop model on the model it was derived from. If you want to fit all the
loop models, regardless of which model they were derived from (not
recommended) then you can simply write your own Python loop that builds
a suitable alignment and calls selection.superpose(). You can see the
code that loopmodel itself uses in
modlib/modeller/automodel/loopmodel.py; see the fit_models_on_template()
method. It should be straightforward enough to adapt that to your needs.