@cyanheads/protein-mcp-server 0.5.3 → 0.7.0

package/dist/mcp-server/tools/definitions/get-structure.tool.js

@@ -2,9 +2,12 @@
  * @fileoverview protein_get_structure — fetch experimental, predicted, or
  * best-available structures by ID. Batches up to N experimental IDs in one RCSB
  * GraphQL call with per-ID partial success (`failed[]`). Optionally inlines
- * coordinate-file content; when that overflows a byte budget it returns a
- * per-structure section outline for targeted re-call instead of truncating.
- * Carries upstream data attribution (RCSB PDB / AlphaFold DB) per response.
+ * coordinate-file content; when that overflows a byte budget the content is
+ * withheld from both surfaces and a per-structure size outline is returned
+ * instead of truncating. Every success-path advisory — batch cap, partial
+ * failure, overflow, failed inlining — accumulates into one notice, since the
+ * framework's `notice` field is last-write-wins. Carries upstream data
+ * attribution (RCSB PDB / AlphaFold DB) per response.
  * @module mcp-server/tools/definitions/get-structure.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -18,7 +21,7 @@ import { mapWithConcurrency } from '../../../services/shared/async.js';
 import { attributionsFor } from '../../../services/shared/attribution.js';
 import { fetchText } from '../../../services/shared/http.js';
 import { isAlphaFoldEntryId, isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
-import { attributionSchema, renderAttribution } from './_schemas.js';
+import { attributionSchema, ligandSchema, polymerEntitySchema, renderAttribution, } from './_schemas.js';
 const confidenceBucketsSchema = z.object({
     veryLow: z.number().describe('Fraction of residues with pLDDT < 50.'),
     low: z.number().describe('Fraction with pLDDT 50–70.'),
@@ -39,6 +42,22 @@ const structureRecordSchema = z
     method: z.string().optional().describe('Experimental method(s).'),
     resolution: z.number().optional().describe('Resolution in Å (experimental).'),
     organism: z.string().optional().describe('Source organism.'),
+    molecularWeight: z
+        .number()
+        .optional()
+        .describe('Deposited structure molecular weight in kDa, from the RCSB entry record. Omitted when the record does not report one.'),
+    releaseDate: z
+        .string()
+        .optional()
+        .describe('Initial release date (ISO 8601), from the RCSB entry record. Omitted when the record does not report one.'),
+    polymerEntities: z
+        .array(polymerEntitySchema)
+        .optional()
+        .describe('Modeled polymer entities, each with both chain namespaces — authAsymIds for protein_get_annotations.chain, labelAsymIds for protein_compare_structures.chain. Present for records served by the RCSB entry endpoint (source experimental, computed models included); omitted for predicted / best_available records and for entries with none.'),
+    ligands: z
+        .array(ligandSchema)
+        .optional()
+        .describe('Bound non-polymer components. Present for records served by the RCSB entry endpoint; omitted when the entry binds none or the record carries no ligand data.'),
     provider: z.string().optional().describe('Model provider (predicted / best_available).'),
     confidence: z
         .number()
@@ -78,16 +97,7 @@ const structureRecordSchema = z
     .describe('A resolved structure with metadata and coordinate-file URLs.');
 export const getStructure = tool('protein_get_structure', {
     title: 'protein-mcp-server: get structure',
-    description: '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.',
+    description: `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.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -154,15 +164,26 @@ export const getStructure = tool('protein_get_structure', {
             .describe('Present only when inlined coordinates across the batch exceeded the response budget.'),
     }),
     enrichment: {
-        requested: z.number().describe('Number of IDs requested.'),
-        resolved: z.number().describe('Number of IDs resolved.'),
-        notice: z.string().optional().describe('Advisory note (partial failures, overflow guidance).'),
+        requested: z
+            .number()
+            .describe('Number of IDs in the original request (input.ids.length), before the batch cap was applied.'),
+        processed: z
+            .number()
+            .describe('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.'),
+        resolved: z.number().describe('Number of processed IDs that resolved to a structure.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Every applicable advisory joined into one string: batch cap, partial failures, coordinate-budget overflow, and failed coordinate inlining.'),
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
         const ids = input.ids.slice(0, cfg.maxBatchIds).map((s) => s.trim());
+        // `ctx.enrich.notice` is last-write-wins, so a second call erases the first.
+        // Every advisory this handler can raise accumulates here and is written once.
+        const notices = [];
         if (input.ids.length > cfg.maxBatchIds) {
-            ctx.enrich.notice(`Batch capped at ${cfg.maxBatchIds} IDs; ${input.ids.length - cfg.maxBatchIds} ignored.`);
+            notices.push(`Batch capped at ${cfg.maxBatchIds} IDs; ${input.ids.length - cfg.maxBatchIds} ignored.`);
         }
         if (input.source === 'experimental') {
             if (ids.some((id) => isUniProtAccession(id) && !isPdbId(id))) {
@@ -178,6 +199,9 @@ export const getStructure = tool('protein_get_structure', {
         if (structures.length === 0) {
             throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`, { ...ctx.recoveryFor('all_failed') });
         }
+        if (failed.length > 0) {
+            notices.push(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
+        }
         // Inline coordinates when requested (all, or only the re-called sections).
         const inlineSet = input.sections?.length
             ? new Set(input.sections.map((s) => s.toUpperCase()))
@@ -185,34 +209,44 @@ export const getStructure = tool('protein_get_structure', {
                 ? 'all'
                 : null;
         if (inlineSet) {
-            await inlineCoordinates(structures, inlineSet, cfg.fanoutConcurrency, ctx);
+            const inlineFailures = await inlineCoordinates(structures, inlineSet, cfg.fanoutConcurrency, ctx);
+            if (inlineFailures.length > 0) {
+                notices.push(`Coordinate inlining failed for ${inlineFailures.join(', ')}; the metadata is complete but the coordinate content is missing — retry, or download the file from that structure's coordinateUrls.`);
+            }
         }
-        // Overflow guard: inlining several coordinate files at once can blow the
-        // response budget. A single structure always inlines (re-calling for the lone
-        // section would return the same bytes); 2+ over budget collapse to a size index.
+        // Overflow guard: one coordinate file can blow the response budget on its own
+        // (4HHB.cif is ~30× it), so the budget applies to the inlined total however few
+        // files it spans. Over budget the payload is withheld from both surfaces and
+        // `overflow` carries the per-structure size index. A lone withheld file is
+        // pointed at its own coordinateUrls — a `sections` re-call would return the
+        // identical bytes — while a batch keeps the targeted re-call. A `sections`
+        // re-call is not itself re-gated: the caller has already named the exact bytes.
         let overflow;
         if (inlineSet === 'all') {
             const withCoords = structures.filter((s) => s.coordinates);
             const total = withCoords.reduce((n, s) => n + (s.coordinates?.length ?? 0), 0);
-            if (withCoords.length > 1 && total > DEFAULT_OUTLINE_BUDGET_BYTES) {
+            if (total > DEFAULT_OUTLINE_BUDGET_BYTES) {
                 const sections = withCoords.map((s) => ({ id: s.id, bytes: s.coordinates?.length ?? 0 }));
                 for (const s of structures) {
                     delete s.coordinates;
                     delete s.coordinateFormat;
                 }
-                overflow = {
-                    sections,
-                    notice: `Inlined coordinates (${total} bytes across ${sections.length} structures) exceeded the ` +
-                        `${DEFAULT_OUTLINE_BUDGET_BYTES}-byte budget. Re-call with sections:["${sections[0]?.id}"] ` +
-                        `(add more IDs as needed) to inline specific structures.`,
-                };
-                ctx.enrich.notice('Coordinates exceeded the inline budget; re-call with sections for specific structures.');
+                // One string for `overflow.notice` and the enrichment accumulator, so the
+                // structured and text surfaces cannot describe the withheld state differently.
+                const overflowNotice = sections.length === 1
+                    ? `Inlined coordinates for ${sections[0]?.id} (${total} bytes) exceeded the ${DEFAULT_OUTLINE_BUDGET_BYTES}-byte budget and were withheld. Download the file from that structure's coordinateUrls — re-calling for the lone section would return the same bytes.`
+                    : `Inlined coordinates (${total} bytes across ${sections.length} structures) exceeded the ${DEFAULT_OUTLINE_BUDGET_BYTES}-byte budget. Re-call with sections:["${sections[0]?.id}"] (add more IDs as needed) to inline specific structures.`;
+                overflow = { sections, notice: overflowNotice };
+                notices.push(overflowNotice);
             }
         }
-        ctx.enrich({ requested: ids.length, resolved: structures.length });
-        if (failed.length > 0) {
-            ctx.enrich.notice(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
-        }
+        ctx.enrich({
+            requested: input.ids.length,
+            processed: ids.length,
+            resolved: structures.length,
+        });
+        if (notices.length > 0)
+            ctx.enrich.notice(notices.join(' '));
         // Attribution is a per-response union of the sources actually present, keyed
         // off each record's real provider. Experimental data is fetched from RCSB
         // regardless of the beacon's provider label. best_available federates predicted
@@ -234,6 +268,9 @@ export const getStructure = tool('protein_get_structure', {
         };
     },
     format: (result) => {
+        // A structure named in the overflow index had its payload withheld from the
+        // structured surface; the text surface must not render a prefix of it either.
+        const withheld = new Set(result.overflow?.sections.map((s) => s.id) ?? []);
         const lines = [`## Structures (${result.structures.length})`];
         for (const s of result.structures) {
             lines.push(`\n### ${s.id} _(${s.source})_`);
@@ -244,6 +281,8 @@ export const getStructure = tool('protein_get_structure', {
                 s.method ? `**Method:** ${s.method}` : null,
                 typeof s.resolution === 'number' ? `**Resolution:** ${s.resolution} Å` : null,
                 s.organism ? `**Organism:** ${s.organism}` : null,
+                typeof s.molecularWeight === 'number' ? `**MW:** ${s.molecularWeight} kDa` : null,
+                s.releaseDate ? `**Released:** ${s.releaseDate}` : null,
                 s.provider ? `**Provider:** ${s.provider}` : null,
                 typeof s.confidence === 'number'
                     ? `**Confidence:** ${s.confidence}${s.confidenceType ? ` (${s.confidenceType})` : ''}`
@@ -256,6 +295,27 @@ export const getStructure = tool('protein_get_structure', {
                 const b = s.confidenceBuckets;
                 lines.push(`**Confidence:** veryHigh ${pct(b.veryHigh)} · confident ${pct(b.confident)} · low ${pct(b.low)} · veryLow ${pct(b.veryLow)}`);
             }
+            if (s.polymerEntities && s.polymerEntities.length > 0) {
+                lines.push('**Polymer entities:**');
+                for (const e of s.polymerEntities) {
+                    const parts = [
+                        e.description,
+                        e.organism,
+                        // Both namespaces are labelled, never merged — they are not interchangeable.
+                        e.authAsymIds ? `auth_asym_id: ${e.authAsymIds.join(', ')}` : null,
+                        e.labelAsymIds ? `label_asym_id: ${e.labelAsymIds.join(', ')}` : null,
+                        typeof e.sequenceLength === 'number' ? `${e.sequenceLength} residues` : null,
+                    ].filter(Boolean);
+                    lines.push(`- **${e.entityId}** — ${parts.join(' · ')}`);
+                }
+            }
+            if (s.ligands && s.ligands.length > 0) {
+                lines.push('**Ligands:**');
+                for (const l of s.ligands) {
+                    const parts = [l.name, l.formula].filter(Boolean);
+                    lines.push(`- **${l.compId}**${parts.length > 0 ? ` — ${parts.join(' · ')}` : ''}`);
+                }
+            }
             const urls = [
                 s.coordinateUrls.cif ? `[cif](${s.coordinateUrls.cif})` : null,
                 s.coordinateUrls.pdb ? `[pdb](${s.coordinateUrls.pdb})` : null,
@@ -265,7 +325,10 @@ export const getStructure = tool('protein_get_structure', {
                 lines.push(`**Coordinates:** ${urls.join(' · ')}`);
             if (s.paeDocUrl)
                 lines.push(`**PAE:** ${s.paeDocUrl}`);
-            if (s.coordinates) {
+            if (withheld.has(s.id)) {
+                lines.push('**Coordinates withheld** — over the inline budget; see the URLs above.');
+            }
+            else if (s.coordinates) {
                 lines.push(`**Inlined ${s.coordinateFormat ?? 'coordinates'} (${s.coordinates.length} bytes):**`);
                 lines.push('```', s.coordinates.slice(0, 2000), s.coordinates.length > 2000 ? '… (truncated in text view)' : '', '```');
             }
@@ -315,7 +378,15 @@ async function fetchExperimental(ids, ctx) {
             ...(meta.title ? { title: meta.title } : {}),
             ...(meta.methods && meta.methods.length > 0 ? { method: meta.methods.join(', ') } : {}),
             ...(typeof meta.resolution === 'number' ? { resolution: meta.resolution } : {}),
+            ...(typeof meta.molecularWeight === 'number'
+                ? { molecularWeight: meta.molecularWeight }
+                : {}),
+            ...(meta.releaseDate ? { releaseDate: meta.releaseDate } : {}),
             ...(meta.organisms.length > 0 ? { organism: meta.organisms[0] } : {}),
+            // Already on EntryMeta from the same getEntries() call — omitted rather than
+            // emitted empty, so a sparse entry does not read as "this entry has none".
+            ...(meta.polymerEntities.length > 0 ? { polymerEntities: meta.polymerEntities } : {}),
+            ...(meta.ligands.length > 0 ? { ligands: meta.ligands } : {}),
             coordinateUrls: {
                 cif: rcsb.coordinateFileUrl(meta.id, 'cif'),
                 pdb: rcsb.coordinateFileUrl(meta.id, 'pdb'),
@@ -436,9 +507,15 @@ function coordinateUrlFor(url) {
         return { pdb: url };
     return { cif: url };
 }
-/** Fetch and inline coordinate content for the requested structures. */
+/**
+ * Fetch and inline coordinate content for the requested structures. Returns the
+ * IDs whose fetch failed — a record that silently lacks `coordinates` is
+ * indistinguishable from one that was never asked to inline, so the caller needs
+ * the failure named in the response rather than only in the log.
+ */
 async function inlineCoordinates(structures, inline, concurrency, ctx) {
     const targets = structures.filter((s) => inline === 'all' || inline.has(s.id.toUpperCase()));
+    const failures = [];
     await mapWithConcurrency(targets, concurrency, async (s) => {
         const pick = s.coordinateUrls.cif
             ? ['cif', s.coordinateUrls.cif]
@@ -461,7 +538,9 @@ async function inlineCoordinates(structures, inline, concurrency, ctx) {
                 id: s.id,
                 error: err instanceof Error ? err.message : err,
             });
+            failures.push(s.id);
         }
     });
+    return failures;
 }
 //# sourceMappingURL=get-structure.tool.js.map

package/dist/mcp-server/tools/definitions/get-structure.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts

@@ -61,6 +61,11 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
     readonly code: JsonRpcErrorCode.InvalidParams;
     readonly when: "No query, sequence, organism, method, or maximum resolution was provided — nothing to search on.";
     readonly recovery: "Provide a free-text query, protein sequence, organism name, experimental method, or maximum resolution.";
+}, {
+    readonly reason: "sequence_modifier_without_sequence";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "min_identity or max_evalue was supplied with no sequence, so the threshold would never reach a sequence search.";
+    readonly recovery: "Add a sequence to run a similarity search these thresholds can filter, or drop min_identity and max_evalue and search on the remaining criteria.";
 }, {
     readonly reason: "duplicate_dimension";
     readonly code: JsonRpcErrorCode.InvalidParams;

package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsP3B,CAAC"}
+{"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwDjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsR3B,CAAC"}

package/dist/mcp-server/tools/definitions/search-structures.tool.js

@@ -30,6 +30,24 @@ function isPredictedId(id) {
 function accessionFromCsm(id) {
     return /AF_AF([A-Z0-9]+?)F\d+$/i.exec(id)?.[1]?.toUpperCase();
 }
+/**
+ * Advisory for the facet dimensions the bucket cap sliced, naming every one of
+ * them rather than the first. The cap here is fixed server-side with no per-call
+ * override, so the route to the long tail is another tool: every dimension this
+ * tool facets is also a `protein_analyze_collection` `group_by` value, and that
+ * tool takes a `bucket_limit` up to 500.
+ *
+ * A sequence search has no such route — `protein_analyze_collection` has no
+ * sequence input, so it cannot reproduce the result set the facet describes.
+ * Pointing there would hand back a different distribution under the same name,
+ * so that case is told to narrow the request instead.
+ */
+function truncationNotice(dimensions, cap, sequenceSearch) {
+    const named = `${dimensions.join(' and ')} ${dimensions.length > 1 ? 'were' : 'was'} capped at ${cap} buckets`;
+    return sequenceSearch
+        ? `${named}. protein_analyze_collection cannot reproduce a sequence search, so narrow this request instead: drop sequence, or add organism, method, max_resolution, or query filters to shrink the distribution before the cap.`
+        : `${named}. Call protein_analyze_collection with ${dimensions.length > 1 ? 'each dimension' : 'that dimension'} in group_by and a bucket_limit above ${cap} (up to 500) to reach the long tail.`;
+}
 export const searchStructures = tool('protein_search_structures', {
     title: 'protein-mcp-server: search structures',
     description: 'Search experimental (PDB) and predicted (computed-model) protein structures by free text, ' +
@@ -49,6 +67,12 @@ export const searchStructures = tool('protein_search_structures', {
             when: 'No query, sequence, organism, method, or maximum resolution was provided — nothing to search on.',
             recovery: 'Provide a free-text query, protein sequence, organism name, experimental method, or maximum resolution.',
         },
+        {
+            reason: 'sequence_modifier_without_sequence',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'min_identity or max_evalue was supplied with no sequence, so the threshold would never reach a sequence search.',
+            recovery: 'Add a sequence to run a similarity search these thresholds can filter, or drop min_identity and max_evalue and search on the remaining criteria.',
+        },
         {
             reason: 'duplicate_dimension',
             code: JsonRpcErrorCode.InvalidParams,
@@ -83,12 +107,12 @@ export const searchStructures = tool('protein_search_structures', {
             .min(0)
             .max(1)
             .optional()
-            .describe('Minimum sequence identity (0–1) for a sequence search. Default 0.'),
+            .describe('Minimum sequence identity (0–1) for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold would never reach RCSB. Default 0.'),
         max_evalue: z
             .number()
             .positive()
             .optional()
-            .describe('Maximum E-value for a sequence search. Default 1.'),
+            .describe('Maximum E-value for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold would never reach RCSB. Default 1.'),
         content_type: z
             .enum(['experimental', 'predicted', 'all'])
             .default('all')
@@ -166,6 +190,18 @@ export const searchStructures = tool('protein_search_structures', {
                 ...ctx.recoveryFor('no_criteria'),
             });
         }
+        // buildQuery() reads these two only inside its sequence branch, so without a
+        // sequence they never reach RCSB and the response looks like a filtered search
+        // that was never filtered. Rejected here rather than in the schema so the
+        // caller gets a data.reason and the declared recovery hint alongside -32602.
+        const sequenceModifiers = [
+            typeof input.min_identity === 'number' ? 'min_identity' : undefined,
+            typeof input.max_evalue === 'number' ? 'max_evalue' : undefined,
+        ].filter((name) => name !== undefined);
+        if (!input.sequence && sequenceModifiers.length > 0) {
+            const many = sequenceModifiers.length > 1;
+            throw ctx.fail('sequence_modifier_without_sequence', `${sequenceModifiers.join(' and ')} ${many ? 'are sequence-search thresholds' : 'is a sequence-search threshold'}, but this request has no sequence — ${many ? 'they' : 'it'} would never reach RCSB.`, { ...ctx.recoveryFor('sequence_modifier_without_sequence') });
+        }
         // RCSB collapses two identically-named facet requests into one raw facet, and
         // the attribute-keyed lookup maps both specs back onto it — a repeated
         // dimension would return the same breakdown twice and double-count on any sum.
@@ -207,13 +243,17 @@ export const searchStructures = tool('protein_search_structures', {
         });
         if (input.query)
             ctx.enrich.echo(input.query);
-        // `notice` is a single last-wins field, so the zero-hit advice and one
-        // fragment per under-covered facet dimension compose into ONE string.
+        // `notice` is a single last-wins field, so the zero-hit advice, the capped-facet
+        // advice, and one fragment per under-covered facet dimension compose into ONE string.
         const notices = [];
         if (hits.length === 0)
             notices.push(ZERO_HIT_NOTICE[input.content_type]);
-        if (facets)
+        if (facets) {
+            const capped = facets.filter((f) => f.truncated).map((f) => f.dimension);
+            if (capped.length > 0)
+                notices.push(truncationNotice(capped, cfg.facetBucketCap, Boolean(input.sequence)));
             notices.push(...coverageNotices(facets, result.total));
+        }
         if (notices.length > 0)
             ctx.enrich.notice(notices.join(' '));
         return { hits, ...(facets ? { facets } : {}) };

package/dist/mcp-server/tools/definitions/search-structures.tool.js.map

@@ -1 +1 @@
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package/dist/services/rcsb/facets.d.ts

@@ -45,6 +45,25 @@ export declare const FACET_DIMENSIONS: {
 export type FacetDimensionName = keyof typeof FACET_DIMENSIONS;
 /** All supported dimension names (for Zod enums). */
 export declare const FACET_DIMENSION_NAMES: [FacetDimensionName, ...FacetDimensionName[]];
-/** Build a {@link FacetSpec} for a dimension, with an optional interval override and nested child. */
+/** The histogram / date-histogram dimensions, in enum order — the set an `interval` can reach. */
+export declare const INTERVAL_DIMENSION_NAMES: ("method" | "molecular_weight" | "organism" | "polymer_type" | "release_year" | "resolution")[];
+/**
+ * Which requested dimension can consume an `interval` override, or `undefined`
+ * when neither can. Compatibility is by value type rather than merely "not
+ * terms": a numeric bin width belongs to a `histogram` dimension, the `year`
+ * period to a `date_histogram` one. The primary position wins when both could
+ * take it, so an ambiguous override lands where the caller can predict.
+ */
+export declare function intervalTarget(interval: number | string, dimension: FacetDimensionName, child?: FacetDimensionName): FacetDimensionName | undefined;
+/**
+ * Build a {@link FacetSpec} for a dimension, with an optional interval override
+ * and nested child. The override reaches whichever of the two positions can
+ * consume it ({@link intervalTarget}) — RCSB honours a per-position `interval`
+ * on a nested facet, so a histogram child is not stuck on its default just
+ * because the parent aggregates by terms. The position that cannot consume it
+ * keeps its own default, and an override no position accepts is dropped rather
+ * than sent upstream; callers that must reject that case ask
+ * {@link intervalTarget} first.
+ */
 export declare function buildFacetSpec(dimension: FacetDimensionName, interval?: number | string, child?: FacetDimensionName): FacetSpec;
 //# sourceMappingURL=facets.d.ts.map

package/dist/services/rcsb/facets.d.ts.map

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