The atom number of RF3 model doesnt match with the atom number of ProteinMPNN

Hello there, thank you for the amazing work.

I have a quesiton that the atom number of RF3 model doesnt match with the atom number of ProteinMPNN. Here is my workflow.

First I ran a rfd3 to generate backbones.
rfd3 design out_dir=/media/user/ALL_USERS/hjd/rfd3/results ckpt_path=~/.foundry/checkpoints/rfd3_latest.ckpt inputs=/media/user/ALL_USERS/hjd/rfd3/JOB.json diffusion_batch_size=500 n_batches=4
The json file looks like this:

{
    "E1": {
        "dialect": 2,
        "infer_ori_strategy": "hotspots",
        "input": "/media/user/ALL_USERS/hjd/rfd3/cleaned_A.pdb",
        "contig": "20-100,/0,A150-420",
        "select_hotspots": {
            "A181": "CG2,CG1",
            "A407": "NE1,CZ2",
            "A214": "NH2,NH1",
            "A404": "CD1,CZ",
            "A222": "CB,CG"

        }
       }
}

Then I ran ProteinMPNN to refine the sequence.

mpnn  \
    --structure_path "${cif_file}" \
    --out_directory "${OUT_DIR}" \
    --checkpoint_path "${CHECKPOINT_PATH}" \
    --model_type protein_mpnn \
    --is_legacy_weights True

After that, I saved all the fa files from last step to a file called "sequences_output.json". And ran RF3.
rf3 fold inputs="./sequences_output.json" ckpt_path="/home/jedi/.foundry/checkpoints/rf3_foundry_01_24_latest_remapped.ckpt" out_dir="./rf3_ouput"
The sequences_output.json file looks like this:
{ "name": "E1_3_model_7_b0_d0(1)", "components": [ { "seq": "GWIEGVVLEFVDDDTVLVDDGERVYRVLRSSVENPENARVGSRVRVSTLTAEEVPVVCPGGTCFSVPTL", "chain_id": "A" } ] }, { "name": "E1_3_model_421_b0_d0(2)", "components": [ { "seq": "MEELVEKIKKKLEAEGYKVLKVKVNEDGTVSVVVEKDGKYYELTFDSKGNLLSKEPVRVVVKVPVNGKATYYKCDCGDSEAGVIFEDYTIPGC", "chain_id": "A" } ] }

The CIF files generated by RF3 have more atoms than the CIF files generated by ProteinMPNN and RFD3. The CIF files have the same length between RFD3 and ProteinMPNN. Is it because RF3 used the B Chain from ProteinMPNN as input? So the CIF model of RF3 is larger?

Many thanks!!!

Start by comparing the RFD3 and ProteinMPNN CIF outputs with the RF3 input in sequences_output.json, then inspect the rf3 fold entry point and the RF3/ProteinMPNN command workflows shown in the report. Reproduce the atom-count difference and determine whether RF3 is folding an unintended chain; done means the source of the extra atoms is identified and documented or corrected.