RosettaCommons
Partial diffusion errors
Hello, I've bumped into a contig error when doing partial diffusion of a PDB composed of chains 'A' and 'B'
When I want to keep fixed chain A but diffuse some residues in chain B by using this contigs code [A1-124/0 B1-2/3-3/B6-121], I get this error: AssertionError: for partial diffusion there can be no offset between the index of a residue in the input and the index of the residue in the output However, I can run the partial diffusion without any problem if I diffuse a random residue in chain A: [A1-123/1-1/0 B1-2/3-3/B6-121] I can also run this: [A1-124/0 B1-121]
We ran into this issue as well when trying to do a similar diffusion process! There's a quirk in the PDB numbering scheme where RFDiffusion outputs get renumbered from the binder going 1-N and the underlying target going N+1-L. This means to get most pdb structures properly formatted you're going to want to attempt to renumber the outputs and potentially rename the chains (RFD names the binder A and B).
