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name: structure-sequences description: "Convert protein structures into SaProt structure-aware amino-acid plus 3Di sequences and diagnose Foldseek and pLDDT masking issues." disable-model-invocation: true metadata: disco-role: operating license: MIT

Structure Sequences

Use this sub-skill when an agent needs to convert a PDB or mmCIF protein structure into SaProt input sequences: amino-acid sequence, Foldseek 3Di sequence, or the combined AA+3Di format consumed by SaProt models.

What this covers

• Run Foldseek structureto3didescriptor with chain-name output and convert its AA and 3Di columns into SaProt-ready records.
• Build combined tokens by pairing each amino acid with a lowercase 3Di character, for example M#, Ev, or Qp.
• Mask low-confidence AlphaFold-style regions by replacing the 3Di character with # when pLDDT is below the chosen threshold.
• Convert one or more selected chains and explain chain-name mismatches from Foldseek output.
• Diagnose missing Foldseek binaries, missing structure files, empty Foldseek output, Bio.PDB parser failures, and pLDDT length mismatches.

Bundled converter

Use the bundled converter instead of importing SaProt repository utilities:

python scripts/convert_structure_sequence.py \
  --foldseek foldseek \
  --structure protein.cif \
  --chain A \
  --plddt-mask auto \
  --output-json protein.sequence.json \
  --output-fasta protein.sequence.fasta

Important arguments:

• --foldseek points to an executable Foldseek binary or to a command available on PATH.
• --structure is a .pdb or .cif structure file readable from the current working directory.
• --chain is repeatable; omit it to emit every chain Foldseek reports.
• --plddt-mask accepts auto, true, or false; use true for AlphaFold-style structures when low-confidence residues should be masked.
• --plddt-threshold defaults to 70.0 and controls when a 3Di position becomes #.
• --seq-type controls FASTA output: combined, aa, or foldseek.

See references/sequence-formats.md for token and masking details, and references/troubleshooting.md for failure handling.

Boundaries and routing

• If a combined sequence already exists and the task is mutation scoring, embeddings, or model loading, route to model-inference.
• If the task is storing converted sequences in LMDB or wiring dataset configuration fields, route to datasets-configs.
• If the task is launching fine-tuning, pretraining, or evaluation runs, route to training-evaluation.
• Do not depend on original repository paths at runtime; copy or call the bundled converter from this sub-skill.