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? I tried this but the resulting model did not preserve the quaternary architecture of the homologous template (the two additional domains were rigidly moved away). I thought a good idea would be to use as input model (inifile) the X-ray structure of my target protein and refine the two additional models using the whole homologous proteins as template. I also defined the selection to model as explained in:  https://salilab.org/modeller/9.23/manual/node23.html

Anyway I got the following:

No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " ", chain " "; atom file name:  INI_MOD.pdb  

(Where INI_MOD.pdb is the input model defined in inifile)
Why did I get this?
Thank you very much for your support,

Stefano 

Il giorno mar 25 feb 2020 alle ore 22:59 Modeller Caretaker <modeller-care@salilab.org> ha scritto:
On 2/25/20 7:26 AM, Stefano Motta wrote:
> I'm trying to build a model of a hetero-dimer starting from an X-ray
> structure. Each monomer have 3 domains (6 in total). An X-ray structure
> of part of the complex (two domains of each monomer) exist and I want to
> complete the model with the two missing domains (one for each monomer).
> I would use the X-ray of homologous proteins for which all 6 domains are
> available. Which would be the best approach? I want to keep the X-ray
> part as frozen as possible, and only model the two missing domains from
> the template (both structure and orientation in the complex).

This should a straightforward application of multiple-template modeling.
You may just need to manually modify the alignment if you get conflicts
(e.g. don't align the model with the 6-domain template in some regions
if it doesn't align well with your X-ray structure).

        Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             https://salilab.org/modeller/
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--
________________________________________________________________

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).
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