Re: [modeller_usage] loop modeling

On 8/15/19 6:44 PM, Rui Chen wrote: > 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.

Ben Webb, Modeller Caretaker