[modeller_usage] How to discard overhangs in target sequence

Hello modellers,

if my target sequence is longer compared to the template sequence and in the alignment I find an overhang for the target sequence at the N- and C-terminus, is there any way to tell modeller by some parameters to use only the part of the target sequence covered by the template, or do I have to cut the overhang in the alignment?

Thanks,

Markus.