Hello,
i´ve had this problem a few times now. Everytime i execute the example recipe 4 "local wiggle", all secondary structure information (helices, beta sheets) is gone. The View setting is still "cartoon", but you can´t adjust distinct domains, e.g. straighten out a helix. Even if i change the view and change it back to "cartoon" again, nothing changes. Why is this? Thanks for any help :)
This happens because the recipe intentionally turns the entire puzzle into loops. Workarounds include saving the secondary structure information and reloading it afterward or restoring the secondary structure manually. Alternatively, you can modify the recipe by removing the instruction that turns the entire puzzle into loops.
It is not a bug, changing to all loops is part of this script.
You just need save structure b4 you run it (no GUI scripting function for that)