Hi Markus, you might modify your alignment like this: >P2;template -----------------YYYYYYYY------------------ >P1;target XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX should become >P2;template -----------------YYYYYYYY------------------ >P1;target -----------------XXXXXXXX------------------ i.e. you might simply delete all parts from the target sequence that you do not want to be modelled. Hope this helps, Oliver Markus Fischer wrote: > 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. > > -- _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific St Seattle, WA 98195 T:(206)685-7046 _______________________________________