Hi, I am modelling a protein 763 amino acids long. There aer no templates available for this protein to thread the sequence onto. The 3D structure of a part of the protein (1 out of 4 domains), however, has been elucidated by NMR spectroscopy. My protein also contains the well-known homeobox domain. I have tried modelling the protein using an alignment with a template obtained from mGenThreader (as shown in the difficult-example tutorial). But the structures obtained by this method show no resemblance to the homeobox domain in the region known to contain the homeobox domain. Is there a way I can incorporate these known structures along with the template obtained from mGenThreader? Please help.

Thanking you Joydeep Mitra

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