In Rosetta, a FoldTree is a representation of the connectivity of a structure. Though for each Rosetta application a foldTree is generated by default, for specific purposes, one might want to generate a custom foldTree (further reading on the FoldTree and a FoldTree tutorial are highly recommended).
A custom FoldTree can be defined through a FoldTree file and provided to Rosetta either via the command-line (using the
-fold_tree flag) or via the RosettaScripts interface, e.g. through the AtomTreeMover
FOLD_TREE EDGE <start position> <stop position> <edge type> EDGE <start position> <stop position> <edge type>
Where start and stop position are the Rosetta internal numbers of the boundary positions that define a segment. edge type can be -1, which specifies a "polymeric" edge (where a chain of residues are connected by covalent bonds), -2, which specifies a covalent "non-polymeric" edge (where the two connected atoms need to be specified after the edge type, ordered according to the specified residues) or a positive integer number specifying a jump number.
This FoldTree defines a structure of the following properties:
FOLD_TREE EDGE 1 18 -1 EDGE 18 32 1 EDGE 32 19 -1 EDGE 32 50 -1 EDGE 50 163 2 EDGE 163 51 -1 EDGE 163 164 -2 C1 SG