PDBsum

5-30 minutesPaperCodeProduction Ready

Generate overview and schematic diagrams of protein chains, DNA, ligands, and metal ions

Readiness

Readiness: Production Ready
Smoke: direct_slurm_passed_with_warnings
Artifacts: not_applicable
Production: production_ready_api_slurm_pdbsum1_html_report
Storage: <5
Strategy: compiled/binary SIF or shared python312_slim + ext3 overlay
Next: Production Ready. Optional hardening: install/configure PyMOL/ImageMagick/template assets to remove PDBsum cleft thumbnail warnings.

No obvious large model/database dependency identified; validate upstream docs before install. 2026-07-05 triage: PDBsum needs official PDBsum1 archives/data/exe/docs staged before a real smoke; no runner adapter is present yet. 2026-07-05 SOP batch recheck: backend inventory found no staged PDBsum1 package/data/executables/docs, SIF, artifacts, or runner. PDBsum remains a source/bootstrap task rather than a storage task; no direct Slurm PDB smoke has run. Kept Smoke Pending. 2026-07-05 18:21 +08:00 backend re-audit: no staged PDBsum source/package/data/docs/SIF/artifacts/runner found under shared backend root; live SIF inventory still only has python312_slim, ubuntu2404, and proteinmpnn_ddg base. Kept Smoke Pending. 2026-07-05 22:44 +08:00 backend implementation pass: staged official RomanLas/PDBsum1 repository rev 5aba7e4936644fe5dbcbc76891db37404309d31b under /media/nik/seagate_nik/bio_server/tools/pdbsum and extracted pdbsum1/data/docs/exe_linux. Seagate filesystem rejected one colon-containing template filename during extract, but direct Slurm job 431 completed core PDBsum1 v1.0.1 sample analysis with run-local CATHPARAM, generated results/index.html and copied/processed 1crn PDB artifacts under /media/nik/seagate_nik/bio_server/runs/pdbsum/sample_clean_20260705_224400. Optional ImageMagick/PyMOL/template warnings remain; reclassified to Runner Adapter Pending pending runner/API adapter and optional dependency hardening. 2026-07-08T20:55:20+08:00: Production Ready promotion: backend runner API job f960f1bdca43 / Slurm job 565 completed through the web runner API using official PDBsum1 rev 5aba7e4936644fe5dbcbc76891db37404309d31b. Adapter writes run-local CATHPARAM, invokes exe_linux/pdbsum1 with -noras on the 1CRN benchmark, and produced zero-byte Slurm stdout/stderr, summary.json, results.csv with ok=TRUE, pdbsum_index.html, and results/index.html containing '1 structure processed'. Known limitation: optional PyMOL/ImageMagick/cleft thumbnail generation remains disabled/missing and emits non-fatal tool stderr warnings; core PDBsum HTML report is generated and downloadable.