[modeller_usage] Modeling multiple domains

[randalla AT uci.edu]

Hello-

Is there a way to force/encourage Modeller to join domains in a manner
with few or no clashes/atom overlaps between domains?

My first test modeling a multiple domain protein, just as in the example
from FAQ #1, resulted in a model with many clashes between the CAs and
other atoms of the domains.

I realize that Modeller cannot correctly predict domain orientation, but I
hope there is a way to strongly discourage inter-domain clashes.

Thanks,

Arlo Randall
University of California, Irvine