Conditioning on protein of different length than protein to be designed

[sweatyaiguy]

Hello and great job on the tool! I'm trying to make a substructure conditioner based on one region of protein A and apply that to a similar region of protein B. However, because the proteins A/B have different numbers of atoms (I specified the same number of residues), I keep getting an error relating to tensor mismatch. Is there an intelligent way to pad/trim the pdbs so that I can do this?

Thanks!

[sweatyaiguy]

Hello! Just wanted to ask again if there's any guidance I could get here.