sir my name is arul and doing molecular modeling using modeller.sir iam modeling two proteins one of my target protein has 35% similarity and other have 55% similarity with their respective templates.sir for running the modeller as i have to give three input files namely script file ,pdb file,alignment file. sir my questions are 1.if if want to create my own alignment file how should i create which has low similarity how should i create. 2.shall i can run modeller for the protein with high similarity by allowing modeller itself to create alignment thanks with regards arul