feat: auto-detect AlphaFold version in chimerax-plot from dataset contents#103
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The chimerax-plot subcommand reconstructs the PDB filename from the --af_version CLI option (default 6), but the Nextflow pipeline never forwards that option and MANE builds force v4. Result: when a user runs chimerax-plot against a v4 dataset without passing --af_version, every candidate PDB path 404s and the script silently skips every gene with no output. Inspect <datasets_dir>/pdb_structures/ at runtime and pick the AF version actually present. The user-supplied --af_version is used only as a tiebreaker when multiple versions coexist; otherwise it's a hint at best. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
This PR fixes chimerax-plot failing to find any PDBs when the dataset was built with a different AlphaFold DB version than the CLI default by detecting the version directly from the dataset’s pdb_structures/ directory.
Changes:
- Added
detect_af_version()helper to scan<datasets_dir>/pdb_structures/for*-model_v<N>.pdb[.gz]files and select the appropriate AlphaFold version. - Updated
generate_chimerax_plot()to use the detected version (using--af_versiononly as a tiebreaker when multiple versions exist).
Reviewed changes
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| File | Description |
|---|---|
| scripts/plotting/utils.py | Adds AlphaFold version detection logic by inspecting filenames in pdb_structures/. |
| scripts/plotting/chimerax_plot.py | Uses detected AlphaFold version before constructing candidate PDB paths. |
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Summary
chimerax-plotreconstructs PDB filenames asAF-<id>-F<n>-model_v<af_version>.pdb, takingaf_versionfrom a CLI flag (default6). The Nextflow pipeline never forwards--af_version, and MANE builds force v4 — so against a v4 dataset, every PDB lookup fails and the script silently skips every gene with no output.Inspect
<datasets_dir>/pdb_structures/at runtime and pick the AlphaFold version actually present. The user-supplied--af_versionis now used only as a tiebreaker when multiple versions coexist.