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