I'm trying to model a protein that looks like a member of CIS_IPPS with
reasonable homlogy for a major portion of the sequence, but with a
significant insertion region that has weak homology to a portion of a
different protein. I tried to build with the .py & .ali files listed
below, with the result that the CIS_IPPS regions of the protein were
built just fine, but the insertion region was nothing but a random coil.
When I extracted the insertion region & modeled it based on the
extracted portion of the other protein, I was able to model something
reasonable. I could use a GUI to meld the two models together, but I'd
rather have recommendations as to how to get modeller to do the build
for me - I think it'd be a lot better starting structure than the result
of a hand-meld.