What is the best way to define a custom fold tree?
I find that -auto_setup_metals does not work for me and I'd like to set up my fold tree manually.
If you're using RosettaScripts, you can specify the fold tree with the AtomTree mover (https://www.rosettacommons.org/docs/latest/protein-interface-design-move...)
If you're using another protocol, you'll have to look for protocol-specific options to specify the fold tree. In general, there isn't a way to specify an arbitrary fold tree. (Although some protocols will obey an input foldtree from a silent file, so you could create a silent file with a particular foldtree with RosettaScripts and the AtomTree mover, and then use that silent file as input instead of the PDB.)