Hi all, a colleague in our lab has recently characterized 5 different variants of a transmembrane G Protein-Coupled Receptor with a substantially long N-terminus, and we are now at the point where we want to make a figure for her manuscript to showcase the differences in the 3D structures (nothing too complicated, or so I thought). Previously, we had used SWISS Model to approximate our GPCR sequences to a known solved template. However, from what I understand about SWISS Model, it appears that the template automatically is selected based off matching length of the sequence, rather than the contents of the actual sequence. Therefore, if I have two receptor sequences that are identical except one of them has an extra amino acid in the middle of the sequence, SWISS Model selects two completely different templates from which to approximate the models, making them incomparable.

All I want to do is use the same template to approximate the 3D structure of these 5 variants, and maybe highlight in color the parts of the sequence that differ, but I can do that part in iCn3D.

Can anyone with SWISS Model experience recommend a workaround, or recommend a different software to accomplish this task?

Thanks!