I've been trying to trial designing antibody CDRs. Thus far I haven't had much luck applying standard methods. I've converted my antibody to AHO scheme with PyIgClassify and applied the cleanATOM method, however, I am still running into the following error prompt. Any recommendations on how to resolve this, would be great.
I've applied the AntibodyInfo method and am able to print the antibody with the sequences of each CDR, so I don't think the first portion about start and end not being contained is correct.
The prompt says I can apply a loop modeling application to fix the issue, so I'm reading a bit about what's possible from the documentation and pyTutorial. Any thoughts or suggested reading is appreciated.
Antibody does not contain the start or end residue of cdr loop H1 start: 132 end: 0 Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB. This could also mean missing density in the cdr loop. Loop modeling applications can be used to fill missing residues
Have you set the numbering schemes on the command line (or pyRosetta equivalent)? https://new.rosettacommons.org/docs/latest/application_documentation/antibody/General-Antibody-Options-and-Tips
My other suggestion is to simplify your setup as much as possible. Turn on/off design; try a different CDR; specify another set of CDR clusters.
Rosetta is prone to not working in edge cases as a consequence of its development cycle. (Trainee creates new functionality to solve a specific scientific problem. Generalizes application to some degree. Keeps edge cases that allow function in their specific system. Graduates. Other edge cases have to be identified and fixed by a new developer.)