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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
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

Phd Student