Pose is full atom and mover expects centroid, how do I handle it the best?

I don’t know about that mover but I can say Centroid is without sidechains. There’s a residue-specific chonky beta carbon as opposed to a sidechain and one hydrogen. You are saying: “I’m trying to use pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader for a project of side-chain packing small peptides with a fixed backbone ” [emphasis added]”

You can apply switch a pose to centroid via `pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover(‘centroid’)` and then recover the sidechains via `pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover` when you switch it back to full atom, sure, but saving the silent file in centroid mode utterly defeats the purpose of your experiment as don;t care about the fixed backbone, but care about your sidechains —so no to #1 and #3.

If this mover is one that accepts other movers (havent checked), then all your movers should return a full-atom pose… if so, maybe one isn’t and that is the root of the problem.

Googling often returns blanks with PyRosetta as it does not catch code well and the scripts you are looking for are in the SI of paywalled papers. A nice way to find more about a mover, beyond the Rosetta scripts page and the PyRosetta Sphinx docs is looking at the tests in the Rosetta download, these are Rosetta scripts though, and the raw code of the mover as going from C++ doxigen to Python docstrings to Sphinx as the former standard is a bit rubbish. And if you are sure you aren’t doing anything beginner-level wrong, then email the author can help!

It is a warning, not an error, but yes, your external_packer is converting your centroid pose to full atom.

I have a notebook called centroid and I see some lines that may be handy, e.g.

assert pose.is_centroid()

assert not pose.is_fullatom()



#



import nglview as nv  # assuming in Jupyter not Colab



view = nv.show_rosetta(pose)

view.add_hyperball()

view.download_image('centroid.png')

view

A centroid pose has odd sidechains.

If you have ligands in Rosetta or with PyRosetta initialisation they require a params file argument for the fa and for the cen. In PyRosetta they will require their residue type to added to the residue type set of the pose.

Most movers and protocols don’t use silent files and when they do they can make it at whatever point was felt best suited, but generally Options are read at the start.