[{"slug":"ZV-2026-0882","server_name":"protein.caseyjhand.com","severity":"breaking","title":"protein.caseyjhand.com: Field cap was removed from protein_analyze_collection output; consumers reading it will break.","summary":"[breaking] Field cap was removed from protein_analyze_collection output; consumers reading it will break. [breaking] Field shown was removed from protein_analyze_collection output; consumers reading it will break. [risky] Description of protein_get_structure changed (35% word delta). [risky] Field processed was added to protein_get_structure output.","changes":[{"kind":"output_property_removed","path":"outputSchema.properties.cap","tool":"protein_analyze_collection","before":{"type":"number","description":"Per-dimension bucket cap that was applied."},"detail":"Field `cap` was removed from `protein_analyze_collection` output; consumers reading it will break.","severity":"breaking"},{"kind":"output_property_removed","path":"outputSchema.properties.shown","tool":"protein_analyze_collection","before":{"type":"number","description":"Buckets returned for the capped dimension."},"detail":"Field `shown` was removed from `protein_analyze_collection` output; consumers reading it will break.","severity":"breaking"},{"kind":"description_changed","tool":"protein_get_structure","after":"Fetch structures with metadata and coordinate-file URLs. source \"experimental\" takes PDB entry IDs (batched in one call), and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come back marked source \"predicted\" with their modelling provider; \"predicted\" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); \"best_available\" takes UniProt accessions and returns the top federated model — the highest-resolution experimental structure if one exists (optimizing resolution, not biological representativeness, so it can return an engineered mutant over the wild-type entry), else the best prediction. Records served by the RCSB entry endpoint also carry polymer entities with both chain namespaces (labelAsymIds for protein_compare_structures, authAsymIds for protein_get_annotations), bound ligands, molecular weight, and release date. Resolves up to the configured batch cap per call with per-ID partial success — missed IDs are listed in failed[], and IDs beyond the cap are reported in the notice. Set include_coords to inline coordinate content; if the inlined bytes exceed the response budget the content is withheld and overflow lists each structure's size — re-call with sections:[ids] for specific structures, or for a single oversized file download it from that record's coordinateUrls.","before":"Fetch structures with metadata and coordinate-file URLs. source \"experimental\" takes PDB entry IDs (batched in one call), and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come back marked source \"predicted\" with their modelling provider; \"predicted\" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); \"best_available\" takes UniProt accessions and returns the top federated model — the highest-resolution experimental structure if one exists (optimizing resolution, not biological representativeness, so it can return an engineered mutant over the wild-type entry), else the best prediction. Resolves up to the configured batch cap per call with per-ID partial success — missed IDs are listed in failed[]. Set include_coords to inline coordinate content; if that overflows, a section outline is returned — re-call with sections:[ids] to inline specific structures.","detail":"Description of `protein_get_structure` changed (35% word delta).","severity":"risky","descriptionDelta":0.34558823529411764},{"kind":"output_property_added","path":"outputSchema.properties.processed","tool":"protein_get_structure","after":{"type":"number","description":"Number of IDs actually processed after the batch cap. Lower than requested means the excess IDs were ignored and never looked up — re-submit them in a follow-up call."},"detail":"Field `processed` was added to `protein_get_structure` output.","severity":"risky"}],"published_at":"2026-09-09T06:27:13.143Z"}]