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    Ivy Biosciences Docs/Tools/Databases/Biotite/Troubleshooting Biotite

    Troubleshooting Biotite

    Fix missing DSSP or OpenMM, FASTA and GenBank parse errors, out-of-memory batches, and RMSD spikes from unmatched chain IDs — and when to retry instead.

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    This page helps you diagnose missing dependencies (DSSP/OpenMM), FASTA/GenBank parsing errors, out-of-memory failures on large batches, and unexpected RMSD spikes during structure alignment.

    Where this code runs

    You cannot open a shell on the platform yourself. The scripts on this page are plain Biotite Python and shell: ask Ivy in chat to run them in the chat's code workspace, which ships Biotite, or run them on your own machine.

    Common issues and fixes

    Missing DSSP/OpenMM Install biotite[full] and confirm system packages are present. In a local environment, add system deps like libxml2-dev if required by your base image.

    FASTA/GenBank parsing errors Ensure files are UTF-8 and contain header lines. Run a preflight check:

    python - <<'PY'
from biotite.sequence.io import load_sequence
import sys

for path in sys.argv[1:]:
    try:
        load_sequence(path, format=None)
        print(f"OK: {path}")
    except Exception as exc:  # noqa: BLE001
        print(f"FAIL: {path} -> {exc}")
PY inputs/sequences/*

    Out-of-memory on large batches Process files one-by-one, avoid loading entire archives into memory, and write partial outputs frequently to outputs/.

    Unexpected RMSD spikes Strip waters/ligands before alignment and ensure chain IDs match between reference and mobile structures.

    Logging tips

    • Log input counts, skipped files, and final output paths.
    • Capture Biotite version and dependency versions at startup for reproducibility.
    • Add a lightweight summary JSON (counts, errors) alongside outputs.

    When to retry vs. fail fast

    • Retry: network fetch errors or transient PyPI outages during install.
    • Fail fast: missing mandatory inputs, empty sequences, or unsupported residue codes.

    Biotite

    Back to the tool overview.

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    Structure workflows

    Load PDB and mmCIF with Biotite, superpose for RMSD, split chains into per-chain PDB files, and export mmCIF — stripping waters and ligands first.

    Validation & QA

    Preflight Biotite inputs — FASTA headers, non-empty sequences, valid residue codes — then record counts, skipped files and RMSD stats in a SUMMARY.json.

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