FoldTree Terms

Jump

In Rosetta, a Jump represents a rigid-body transformation between two parts of a molecular system, like two protein chains, a protein and a ligand, or two disconnected sections of the same chain. This concept is tied to the FoldTree, which describes the kinematic relationships between residues in a Pose.

A Jump is a single degree of freedom in the kinematic tree. Instead of a series of single-bond torsions, a Jump consists of six degrees of freedom: three for rotation and three for translation. This allows for the movement of entire rigid bodies relative to one another.

Common scenarios whereJumps are used include:

• Protein-protein interfaces: Each chain in a multi-chain Pose is typically treated as a rigid body, with Jumpsconnecting the chains.
• Protein-ligand complexes: The ligand is treated as a separate rigid body connected to the protein by aJump.
• Modeling loops: By introducing a virtual Jump and a “chain break”, Rosetta can effectively sample the conformational space of a protein loop while keeping the rest of the protein fixed.