Issues with chain numbering in disulfide bonds

[jamaliki]

Hi,

Thank you for your wonderful program. I am having issues with a nanobody structure, keeping the frameworks regions and diversifying the CDR loops. I believe due to the proximity of the main chain because of the existence of a disulfide bond, the numbering scheme is getting confused. Is there a way to force this to be the same as the input PDB? I have attached a sample nanobody and the command I am using. I have also attached a sample output so that you can see the problem.

./scripts/run_inference.py inference.output_prefix=nanobody_binders/nanobody_binders inference.input_pdb=../nanobody.pdb 'contigmap.contigs=[X1-25/7-10/X33-98/12-15/X111-121]' inference.num_designs=1000 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0

nanobody_input.pdb.zip rf_diffusion_output.pdb.zip

Best, Kiarash.