You seem to be exploring things the developers haven’t tried yet. Here is what Ingemar (the symmetry author) has to say:
“
this is hard for me to respond to because I don’t know if the membrane scoring function is compatible with symmetry (he is using -abinitio:membrane etc). If not, then all sorts of weird artifacts can happen. I know someone in the Bakerlab has used fnd to fold membrane proteins but I don’t know if they used the membrane scoring function. This was Ray Wang in the Baker lab, Yifan might now, and if not Vladimir perhaps?
If the membrane scoring is working with symmetry then I could look at it again.”
I’ve forwarded it along to those he suggested.
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