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,

Stefano  


Il giorno mar 25 feb 2020 alle ore 23:37 Modeller Caretaker <modeller-care@salilab.org> ha scritto:
On 2/25/20 2:33 PM, Stefano Motta wrote:
> Thanks for your answer. Do you mean that I should remove the 4 domains
> present in the X-ray of my target protein from the homologous template?

No. As you discovered you'll lose information that way. I would just
align the two templates together and go from there.

> I thought a good idea would be to use as input
> model (inifile) the X-ray structure of my target protein

That won't work (as you saw) since the inifile has to have exactly the
same sequence as the final model.

        Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage


--
________________________________________________________________

Stefano Motta PhD

Email: stefano.motta@unimib.it
Field of study: Molecular Modeling, and Proteins Molecular Dynamics
 
Università degli Studi di Milano Bicocca
Department of Earth and Environmental Sciences

Piazza dell'Ateneo Nuovo, 1 - 20126, Milano (Italy).
_________________________________________________________________