leaving gaps in non aligned regions

hello modellers, i am trying to model some proteins. but my protein has some region (internal) (15-20 amino acids) which does not have any corresponding region in the template sequence. i DO NOT want to model that region and in my final (3D) strucuture i want to have a gap in the corresponding internal region. other wise that region forms a loop or extended region ( makes the structre ugly ??). i wish to know how my alignement file should look like.... i tried following and did not solve the problem 1) putting " X " for the amino acids for which i dont want the 3D structure to be made 2) puting " - " for the same... waiting for ur reply gowthaman Phd Student ICGEB, India.