MODELLING LOOPS

Hello.

My cuestion is about the loops modelling. I am trying to model the extracelular loops in a protein by searching them in the pdb database. After superposing the small templates for the loop with the model I obtain (by using only one template), I would like to transfer the coordinates from these new templates to the model. However, when I do this, I transfer only a few residues and the rest are put to -999. My cuestion is Is there any way to select only a few residues in the target that I would like to change by tranfering to them the small loop? or should I transfer all the templates at the sime time using the comand TRANSFER XYZ with the apropiate CLUSTER method?

Thanks in advance.