How to generate many confirmation from a given PDB or sequence?

[Y-H-Joe]

Hi Team, thank you for the great work.

How to generate many confirmation from a given PDB or sequence? I hope RFdiffusion can generate a lot of similar structures. I tried

./scripts/run_inference.py inference.input_pdb=cleaned.pdb inference.num_designs=10 inference.output_prefix=rfdiffusion 'contigmap.contigs=[20-20]'

The cleaned.pdb is 20 aa long. But all the generated confirmations are not similar to cleaned.pdb at all.

Could you please tell me what command I should use?

Thank you.

[Y-H-Joe]

Hi Team and Users, I still cannot figure this issue out. My guess is that RFdiffusion is not able to tackle this task. Correct me if I'm wrong. Thanks

[joewatchwell]

So I think your input here isn't doing what you want. The 'contigmap.contigs=[20-20]' input is saying "Make me a random 20 amino acid protein", so the "cleaned.pdb" file isn't being used at all (RFdiffusion never sees it). If you want to try to get different conformations of the sequence contained within cleaned.pdb, you could do:

"contigmap.contigs=[A1-20]" (assuming the cleaned.pdb is chain A, and numbered residues 1-20) And then "contigmap.inpaint_str=[A1-20]" (see the readme for more details about inpaint_str, but this basically diffuses the structure while providing the sequence of the input pdb). Hopefully this will achieve what you want.

We did play with this a while back, and we were for sure about to get diversity in the outputs. We didn't explore it much more than that though :)