RosettaCommons / RosettaCommons/foundry

PDB mirror path not set

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MPNN
Dominant language
Python
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Description

Hi
I am getting this error when trying mpnn sequence design.
Environment variable PDB_MIRROR_PATH not set. Will not be able to use function requiring this variable.

Is this something to worry about? I am using following script as suggested in #121 to run mpnn -

PDB_DIR_PATH="./renamed/"

cif_files=($PDB_DIR_PATH/*.cif)

for file in "${cif_files[@]}"; do
    mpnn --model_type "protein_mpnn" \
    --structure_path "$file" \
    --out_directory MPNN \
    --batch_size 2 \
    --number_of_batches 1 \
    --omit '["CYS"]' \
    --is_legacy_weights "True" \
    --checkpoint_path "/opt/checkpoints/solublempnn_v_48_020.pt"
done

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the code that checks PDB_MIRROR_PATH and trace whether the shown mpnn command requires it for structure_path inputs. Confirm the expected behavior for this script and document or reproduce the required configuration so the warning's impact is clear.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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