The Build Homology Models protocol can build models of a protein sequence using multiple template structures based on a user provided sequence alignment between the model and the templates.

For instance, in the case of two similar templates, protein A and protein B, where one of the loop conformation in protein A is quite different from that in protein B. If we use both templates to build a model, the resulting model in this region would likely resemble a somewhat averaged version of the two.

However if you wish to use only one protein template for this loop region, the option is provided with the parameters Copy From Templates > Protein > Copy Regions.

Select the residues from a specific template protein to specify as Copy Regions. MODELER will build the model using the coordinates of the backbone atoms in this region from the template without further optimization. If the parameter Optimize Sidechains is set to True, all sidechains in Copy Regions will then be optimized.