Fixed Segments in Generated PDB Files Don't Match Reference PDB File about rfdiffusion

[patricia-rocha]

Hi @roccomoretti

After further investigation, I identified the cause of the behavior I described. When RFdiffusion parses the PDB files using the parse_pdb_lines function, it only considers the sequence numbers, excluding any insertion codes. As a result, in my example, (Gly, 52), (Ser, 52A), (Ser, 53) becomes (Gly, 52), (Ser, 52), (Ser, 53). Then, duplicate sequence numbers are removed, leading to the final sequence being (Gly, 52), (Ser, 53), with the insertion (Ser, 52A) discarded.

To address this, I have opted to renumber my files without insertion codes.

[roccomoretti]

I'm unsure how well RFdiffusion works with insertion codes. You can try explicitly including things in the contig (something like [B1-52/B52A-52A/B53-94/14-20/B103-111]), but I haven't tried that at all. You may be better off just renumbering the input file to remove the insertion codes(*). RFdiffusion will renumber/relabel the output structure anyway.

*) Automated methods exist. I'd personally use Rosetta to do it, because that's what I'm familiar with. Other programs will also do it, though.