No. As you discovered you'll lose information that way. I would just
align the two templates together and go from there.
But this means that the four domains for which I have the X-ray of my target would be moved a little and I want to avoid it. Can I tell modeller not to move them?
That won't work (as you saw) since the inifile has to have exactly the
same sequence as the final model.
Indeed I added the two missing domains (manually aligned with the template). In this way my infile has exactly the same residues present in the alignment file for the target sequence, but I expect modeller to refine only the two domains I manually add.
Thank you very much for your support,