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).