It’s worth a shot. The fragments should bias it towards whatever secondary structure it is supposed to be. CCD does not solve to prefer loops, it’s just that it’s used for loops, but is not really smart enough to keep secondary structures intact. Hopefully your fragments will get inserted and nearly close the “loop” and won’t get modified much by the CCD part.
I have asked the abinitio people repeatedly to please document how to do “partial abinitio” as you request (you are not the first person to ask for it) and have never gotten a response. I’m sure it’s possible but I don’t know how. It may be as simple as playing with the movemap; if you want to try editing the C++ code directly we can try to see where the movemap is and tweak it to only allow your regions to change.
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