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The FoldTree

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|foldtree-overview]] and a [FoldTree tutorial] (https://www.rosettacommons.org/demos/latest/tutorials/fold_tree/fold_tree) are highly recommended).

How to pass a FoldTree file

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 | AtomTreeMover]]

File Format

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.

EXAMPLE

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

This FoldTree defines a structure of the following properties:

  • positions that are covalently linked by polymeric connections: 1-18, 19-32 (note inverse order is allowed, as at this point in the file, position 32 is already defined by a jump, whereas 19 is still "detached" from the tree), 32-50, 51-163.
  • positions that are connected by a jump: (1) 18-32; (2) 50-163
  • positions 163-164 are covalently attached through the C1 atom of position 163 and the SG atom of position 164