Hi, I built a homology model of a protein with multiple domains and the templates I used each contain only fragments of the protein obtained from homology modeling.

Now I want to evaluate the stereo chemical quality of the homology model, and compare the values to the templates. but since none of the template contain the whole sequence, I wonder if it make sense to truncate the protein into different domains and only compare the number for the matching domains to the domain?

Thanks
Joyce