low sequence identity

[Margot Ernst <margot.ernst AT univie.ac.at>]

Dear Modeller support,
I am modeling at low sequence identity and I believe to have the following 
problem: The homologous scaffold (comprising a core of beta strands) of my 
target, after a fisrt round of modeling, displays a (suspiciously) low RMSD 
with respect to the template, and a LOT of bad contacts involving the 
hydrophobic core. Consequently I think that in my target secondary structure 
motifs should be arranged more spaciously. How can I accomplish this in terms 
of additional modeling restraints, or chopping up the alignment and modeling 
in pieces, or whatever will work?
thanks,
	margot