I am using Chimera (Modeller) to model a loop, which locates at the
C-termini of the original crystal structure. The structure of the target
protein is a homodimer, however, I cannot model the two chains together.
How can I model the two chains together?
I don't know if you can do it in Chimera - you would have to ask the
Chimera folks. It is definitely possible in Modeller directly though -
just specify both loop segments in your loop modeling script. See
https://salilab.org/modeller/9.22/manual/node36.html in particular the
commented-out "Too loops simultaneously" part of the script.