PDB mirror path not set

[dhiraj82]

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

[Ubiquinone-dot]

The warning atomworks gives is fine, is it throwing an explicit error?

[dhiraj82]

This is the error message I am getting. it is still producing the output, .fa and .cif file. Although I am not able to visualize .cif file using pymol.

Environment variable PDB_MIRROR_PATH not set. Will not be able to use function requiring this variable. To set it you may:
(1) add the line 'export VAR_NAME=path/to/variable' to your .bashrc or .zshrc file
(2) set it in your current shell with 'export VAR_NAME=path/to/variable'
(3) write it to a .env file in the root of the atomworks.io repository

[nscorley]

What happens in PyMol when you try to visualize the file?

That warning shouldn't be blocking, it just is saying it can't find a local PDB mirror (which is required for some functionality, e.g., training models)

[dhiraj82]

Pymol just doesn't show any thing. no error, nothing. however chimera X is showing following error -
Failed opening file xxx.cif:
mmCIF parsing error: expected data value after data name, not unquoted left square bracket on line 6026

and this is line 6026 -

_mpnn_input.remove_ccds []