[modeller_usage] exposed core in generated structures

["Daniel Sullivan" <>]

Hello all-

I have a series of models that I'm looking to analyze.  It seems that
in many cases, the models that have been created have surface
pockets/holes exposing a small portion of the hydrophobic core that
are unexpected (given the template structures) and which I believe to
be artifacts to the modeling process.  The alignments are good, and
I've been unable to come up with a way to get rid of these holes.  Any
suggestions are more than welcome.  I also have images that I can
email if what I wrote above isn't decriptive enough.