The scripts and input files that accompany this demo can be found in the demos/public directory of the Rosetta weekly releases.

KEYWORDS: DESIGN UTILITIES

This document briefly demos how to use favor_native_residue for Rosetta 3.4 in a fixed backbone context. favor_native_residue is a mode (which debuted in Rosetta 2) that pushes the packer to prefer NOT making a mutation when the mutation is only weakly beneficial. This is useful in design contexts where few mutations are desired.

The fixbb executable does not support favor_native_residue because the implementation is a little tricky. (It could, but it currently does not). The problem is that favor_native_residue uses constraints to do the energy favoring. Constraints must be added to the Pose and ScoreFunction. JD2 doesn't instantiate the Pose until after the outer setup of fixbb has already completed, so there is no chance to load the constraints into fixbb.

To run the demo:

$> $ROSETTA3/bin/rosetta_scripts.default.linuxgccrelease @inputs/options

where $ROSETTA3=path-to-Rosetta/main/source

The options file is annotated.

The XML file (inputs/favor_native_residue.xml) contains two movers.
FavorNativeResidue, applied before the packing mover, causes the favor-native-residue behavior. "bonus" is the energy bonus to assign to native residues. 1.5 will likely be overwhelming; 0.5 will be useful; 0.05 will be very weak. You'll have to tune it to your application.