Did you mean that i should edit the template(for missing residues) pdb
so that it contains the co-ordinates of the missing residues only.
Yes (plus a few extra either side of the insertion). Since the alignment
file must match the sequence in the *entire* PDB file, either you need
to include the unused PDB sequence in the alignment (just misalign it so
Modeller doesn't use it in the model - see FAQ #2) which can be a little
awkward, or modify the PDB to remove the unused residues.
But what you mean by overlap the regions a little so that modeller can
figure out the conformation of the missing regions?
If you look at the alignment in my previous email, you'll see that the
model is aligned with both A and B for two residues on each side of each
insertion. If you don't do that, Modeller won't know how to connect the
missing regions with the rest of the protein.