I want to generate a homology model. The full aa sequence of the protein is known and most of the C-terminus of the protein has been crystallized. I performed a BLAST search and I found a protein with some similarity for the N-terminus (~40% but not much overlap with C-terminus). So all I have to do is apply the aa sequence to both models to build my protein...simple right? However when I go to align sequences and templates it really screws up the full aa sequence of my protein of interest - it tries to merge that with the N-terminus protein - resulting in a sequence with 20% identity to the sequence of interest and then tries to overlay one protein on top of the other. In short how do I align the template if I want to keep one protein intact and build on part of the second protein to that structure (do I remove the aas from the redundant part of the second structure). Any help would be appreciated.