Structure-sequence alignment generation with selected PDB how?

Dear structure predictors,

For extracting an alignment with the best template I used HHPred.

Which than predicted a chain of a PDB which is not the best one, because it doesn´t contain an important N-terminal part of my target. 

I would like to use another chain of this PDB but HHPred doesn´t predict it.

Is there a possibility to have a sequence structure alignment between a defined PDB and my target protein sequence with same quality HHPred does?

Many many thanks for reading my post and I appreciate your contribution to solve my problem.

Best

Zsuzsi