Dear Modeller users, I can learn from the Interative Example (Modeller Tutorial) that I can increase the accuracy of the helix strain by removing or transfering the gap to the begining or ending ot the helix. However If my alignment don't have the gap in the helix region and the alignment score seem maximum. I would like to know how I can do in this situation because optimizing the loop cannot be applied in this. This region is in the transmembrane of a membrane protein.

Thank you very much for all of your advices,

My best regards, TriNgo