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. > >