Reply To: using constraints with AbinitioRelax (Rosetta 3.1)

[Anonymous]

I don’t think any of the constraint scores will track that the way you want – they’re all within one pose. There is an RMSD score term that will globally constrain one pose to look like another, but it’s perhaps too simple for your purpose because it only uses the Calpha trace.

When you use CoordinateConstraints, what are the coordinates of the constraints versus the coordinates of the result? You might be able to transform the coordinates for the constraints into the result space to get this to work the way you want. Rosetta’s abinitio might be refusing to allow the whole protein to translate at once (there’s usually no reason to do this), which would cause problems with CoordinateConstraints if the pose’s area of cartesian space is far from the target. But, you can transform the target to be near where Rosetta wants the result to be and it might work?