@cyanheads/protein-mcp-server 0.2.0 → 0.3.0

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

@@ -2,14 +2,17 @@
  * @fileoverview protein_get_annotations — sequence & functional annotation for a
  * protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
  * domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
- * PDB ID to its accession when needed.
+ * PDB ID to its accession when needed — deterministically by default, by author
+ * chain when a multi-chain entry is ambiguous. Carries upstream data attribution.
  * @module mcp-server/tools/definitions/get-annotations.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
+import { attributionsFor } from '../../../services/shared/attribution.js';
 import { isUniProtAccession } from '../../../services/shared/identifiers.js';
 import { getUniProtService } from '../../../services/uniprot/uniprot-service.js';
+import { attributionSchema, renderAttribution } from './_schemas.js';
 const featureSchema = z
     .object({
     type: z.string().describe('Feature type (e.g. Domain, Binding site, Modified residue).'),
@@ -40,12 +43,33 @@ const domainSchema = z
         .describe('Associated GO terms.'),
 })
     .describe('An InterPro domain/family membership with GO terms.');
+const ambiguitySchema = z
+    .object({
+    accessions: z
+        .array(z
+        .object({
+        chain: z
+            .array(z.string())
+            .describe('Author chain IDs (auth_asym_id) this entity covers (e.g. ["A", "C"]).'),
+        accession: z.string().describe('UniProt accession the chains map to.'),
+        proteinName: z.string().optional().describe('Polymer entity description.'),
+    })
+        .describe('One chain-group → UniProt accession mapping within the entry.'))
+        .describe('Every distinct UniProt mapping for the entry, lowest-chain first.'),
+    notice: z
+        .string()
+        .describe('Why multiple mappings exist and how to select one via the chain input.'),
+})
+    .describe('Present only when a PDB ID mapped to more than one distinct UniProt accession and no chain was supplied. The returned accession is the deterministic lowest-chain pick — re-call with chain set to a specific author chain ID to select another.');
 export const getAnnotations = tool('protein_get_annotations', {
     title: 'protein-mcp-server: get annotations',
     description: 'Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), ' +
         'natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a ' +
         "UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's " +
-        'sequence cross-reference. Use the "include" parameter to scope which annotation classes are fetched.',
+        'sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is ' +
+        'deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to ' +
+        'select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries ' +
+        'an "attribution" block with the upstream data licenses and citations.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -54,6 +78,12 @@ export const getAnnotations = tool('protein_get_annotations', {
             when: 'A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.',
             recovery: 'Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.',
         },
+        {
+            reason: 'chain_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.',
+            recovery: 'Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).',
+        },
     ],
     input: z.object({
         uniprot: z
@@ -64,6 +94,10 @@ export const getAnnotations = tool('protein_get_annotations', {
             .string()
             .optional()
             .describe('PDB entry ID; resolved to a UniProt accession via cross-reference.'),
+        chain: z
+            .string()
+            .optional()
+            .describe('Author chain ID (auth_asym_id, e.g. "A") that disambiguates a multi-chain PDB entry to a specific UniProt accession. Case-sensitive — must match the author chain ID exactly (large structures can carry distinct "A" and "a" chains). Only applies with pdb_id; ignored when uniprot is supplied directly. See polymerEntities[].chains in the pdb://{entry_id} resource for an entry\'s author chain IDs.'),
         include: z
             .enum(['features', 'domains', 'variants', 'all'])
             .default('all')
@@ -79,6 +113,12 @@ export const getAnnotations = tool('protein_get_annotations', {
         features: z.array(featureSchema).optional().describe('Structural/functional features.'),
         variants: z.array(featureSchema).optional().describe('Natural sequence variants.'),
         domains: z.array(domainSchema).optional().describe('InterPro domain/family memberships.'),
+        ambiguity: ambiguitySchema
+            .optional()
+            .describe('Alternative UniProt mappings when a PDB ID resolved ambiguously (no chain given).'),
+        attribution: z
+            .array(attributionSchema)
+            .describe('Upstream data-source licenses and citations for every source that contributed to this response. Always present — the attribution obligation travels with the data.'),
     }),
     enrichment: {
         resolvedFrom: z
@@ -92,16 +132,45 @@ export const getAnnotations = tool('protein_get_annotations', {
         const rcsb = getRcsbService();
         let accession = input.uniprot?.toUpperCase();
         let resolvedFrom;
+        let ambiguity;
         if (!accession && input.pdb_id) {
-            const accessions = await rcsb.resolveUniprot(input.pdb_id, ctx);
-            accession = accessions[0];
+            const entities = await rcsb.resolveUniprotEntities(input.pdb_id, ctx);
             resolvedFrom = input.pdb_id.toUpperCase();
+            const chain = input.chain?.trim();
+            if (chain) {
+                const match = entities.find((e) => e.chains.includes(chain));
+                if (!match) {
+                    const available = entities.flatMap((e) => e.chains);
+                    throw ctx.fail('chain_not_found', `Chain "${chain}" matches no UniProt-mapped polymer entity in ${resolvedFrom}.`, {
+                        recovery: {
+                            hint: available.length
+                                ? `Author chains in ${resolvedFrom}: ${available.join(', ')}. Pass one of these, or omit chain for the deterministic default mapping.`
+                                : `${resolvedFrom} exposes no UniProt-mapped protein chains. Pass a UniProt accession directly.`,
+                        },
+                    });
+                }
+                accession = match.accession;
+            }
+            else {
+                // Deterministic default: order entities by their lowest author chain ID and
+                // take the first, so the same entry always yields the same accession
+                // regardless of upstream GraphQL entity ordering. When more than one distinct
+                // accession exists, surface the alternatives so the caller can pick a chain.
+                const ordered = orderByLowestChain(entities);
+                accession = ordered[0]?.accession;
+                const distinct = new Set(entities.map((e) => e.accession));
+                if (accession && distinct.size > 1) {
+                    ambiguity = buildAmbiguity(resolvedFrom, accession, ordered, distinct.size);
+                }
+            }
         }
         if (!accession) {
-            throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.');
+            throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.', { ...ctx.recoveryFor('no_uniprot_mapping') });
         }
         if (!isUniProtAccession(accession)) {
-            throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`);
+            throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`, {
+                ...ctx.recoveryFor('no_uniprot_mapping'),
+            });
         }
         const include = input.include;
         const wantInterPro = include === 'domains' || include === 'all';
@@ -113,6 +182,15 @@ export const getAnnotations = tool('protein_get_annotations', {
         const variants = entry.features.filter((f) => f.category === 'variant');
         const wantFeatures = include === 'features' || include === 'all';
         const wantVariants = include === 'variants' || include === 'all';
+        // Attribution rides with the data. UniProt always contributes on success;
+        // InterPro only when it returned entries; GO only when a returned entry carries
+        // GO terms. InterPro (CC0) and GO (CC BY 4.0) are gated independently — an
+        // InterPro entry can exist with zero GO terms.
+        const sources = new Set(['UniProt']);
+        if (interpro.length > 0)
+            sources.add('InterPro');
+        if (interpro.some((d) => d.goTerms.length > 0))
+            sources.add('GO');
         if (resolvedFrom)
             ctx.enrich({ resolvedFrom });
         return {
@@ -125,6 +203,8 @@ export const getAnnotations = tool('protein_get_annotations', {
             ...(wantFeatures ? { features: toFeatureOutput(features) } : {}),
             ...(wantVariants ? { variants: toFeatureOutput(variants) } : {}),
             ...(wantInterPro ? { domains: interpro } : {}),
+            ...(ambiguity ? { ambiguity } : {}),
+            attribution: attributionsFor(sources),
         };
     },
     format: (result) => {
@@ -140,6 +220,13 @@ export const getAnnotations = tool('protein_get_annotations', {
             lines.push(head.join(' | '));
         if (result.function)
             lines.push(`\n**Function:** ${result.function}`);
+        if (result.ambiguity) {
+            lines.push(`\n### Multiple UniProt mappings`);
+            lines.push(result.ambiguity.notice);
+            for (const m of result.ambiguity.accessions) {
+                lines.push(`- **${m.accession}**${m.proteinName ? ` — ${m.proteinName}` : ''} (chains ${m.chain.join(', ') || 'none'})`);
+            }
+        }
         if (result.features && result.features.length > 0) {
             lines.push(`\n### Features (${result.features.length})`);
             for (const f of result.features)
@@ -158,9 +245,34 @@ export const getAnnotations = tool('protein_get_annotations', {
                     lines.push(`  - ${g.id} ${g.name}${g.category ? ` [${g.category}]` : ''}`);
             }
         }
+        if (result.attribution.length > 0) {
+            lines.push(`\n### Attribution`);
+            lines.push(...renderAttribution(result.attribution));
+        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
+/** Lowest author chain ID for an entity (code-unit order); '' when it has none. */
+function lowestChain(entity) {
+    return [...entity.chains].sort()[0] ?? '';
+}
+/** Order UniProt xrefs by their lowest author chain ID — the deterministic default pick. */
+function orderByLowestChain(entities) {
+    return [...entities].sort((a, b) => lowestChain(a).localeCompare(lowestChain(b)));
+}
+/** Assemble the ambiguity block: every distinct mapping, lowest-chain first, with a notice. */
+function buildAmbiguity(entryId, chosen, ordered, distinctCount) {
+    return {
+        accessions: ordered.map((e) => ({
+            chain: e.chains,
+            accession: e.accession,
+            ...(e.proteinName ? { proteinName: e.proteinName } : {}),
+        })),
+        notice: `${entryId} maps to ${distinctCount} distinct UniProt accessions across its chains. ` +
+            `Returning ${chosen}, the deterministic lowest-chain pick. ` +
+            'Re-call with chain set to a specific author chain ID to select another.',
+    };
+}
 function toFeatureOutput(features) {
     return features.map((f) => ({
         type: f.type,

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

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

@@ -4,6 +4,7 @@
  * 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.
  * @module mcp-server/tools/definitions/get-structure.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -54,6 +55,12 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
         id: z.ZodString;
         reason: z.ZodString;
     }, z.core.$strip>>;
+    attribution: z.ZodArray<z.ZodObject<{
+        source: z.ZodString;
+        license: z.ZodString;
+        citation: z.ZodString;
+        homepage: z.ZodString;
+    }, z.core.$strip>>;
     overflow: z.ZodOptional<z.ZodObject<{
         sections: z.ZodArray<z.ZodObject<{
             id: z.ZodString;

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

@@ -1 +1 @@
-{"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8DjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgOvB,CAAC"}
+{"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgEjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiQvB,CAAC"}

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

@@ -4,6 +4,7 @@
  * 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.
  * @module mcp-server/tools/definitions/get-structure.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -14,8 +15,10 @@ import { getAlphaFoldService } from '../../../services/alphafold/alphafold-servi
 import { getBeaconsService } from '../../../services/beacons/beacons-service.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
 import { mapWithConcurrency } from '../../../services/shared/async.js';
+import { attributionsFor } from '../../../services/shared/attribution.js';
 import { fetchText } from '../../../services/shared/http.js';
 import { isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
+import { attributionSchema, 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.'),
@@ -115,6 +118,9 @@ export const getStructure = tool('protein_get_structure', {
         })
             .describe('A requested ID that did not resolve, with the reason.'))
             .describe('IDs that could not be resolved (partial success).'),
+        attribution: z
+            .array(attributionSchema)
+            .describe('Upstream data-source licenses and citations for every source present in structures[] — RCSB PDB for experimental records, AlphaFold DB for predicted. Always present — the attribution obligation travels with the data.'),
         overflow: z
             .object({
             sections: z
@@ -145,17 +151,17 @@ export const getStructure = tool('protein_get_structure', {
         }
         if (input.source === 'experimental') {
             if (ids.some((id) => isUniProtAccession(id) && !isPdbId(id))) {
-                throw ctx.fail('mixed_id_types', 'source experimental expects PDB entry IDs, but UniProt accessions were present.');
+                throw ctx.fail('mixed_id_types', 'source experimental expects PDB entry IDs, but UniProt accessions were present.', { ...ctx.recoveryFor('mixed_id_types') });
             }
         }
         else if (ids.some((id) => isPdbId(id) && !isUniProtAccession(id))) {
-            throw ctx.fail('mixed_id_types', `source ${input.source} expects UniProt accessions, but PDB IDs were present.`);
+            throw ctx.fail('mixed_id_types', `source ${input.source} expects UniProt accessions, but PDB IDs were present.`, { ...ctx.recoveryFor('mixed_id_types') });
         }
         const { structures, failed } = input.source === 'experimental'
             ? await fetchExperimental(ids, ctx)
             : await fetchPredictedOrBest(ids, input.source, cfg.fanoutConcurrency, ctx);
         if (structures.length === 0) {
-            throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`);
+            throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`, { ...ctx.recoveryFor('all_failed') });
         }
         // Inline coordinates when requested (all, or only the re-called sections).
         const inlineSet = input.sections?.length
@@ -192,7 +198,25 @@ export const getStructure = tool('protein_get_structure', {
         if (failed.length > 0) {
             ctx.enrich.notice(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
         }
-        return { structures, failed, ...(overflow ? { overflow } : {}) };
+        // Attribution is a per-response union of the sources actually present, keyed
+        // off each record's real provider. Experimental data is fetched from RCSB
+        // regardless of the beacon's provider label. best_available federates predicted
+        // models through 3D-Beacons (AlphaFold DB, SWISS-MODEL, BFVD, …), so a predicted
+        // record's provider — not the binary source — determines the credit; an
+        // uncurated provider falls back to an honest no-license entry. Crediting every
+        // predicted model as AlphaFold would mis-attribute a SWISS-MODEL structure.
+        const sources = new Set();
+        for (const s of structures) {
+            sources.add(s.source === 'experimental'
+                ? 'RCSB PDB'
+                : (s.provider ?? '3D-Beacons (provider unspecified)'));
+        }
+        return {
+            structures,
+            failed,
+            attribution: attributionsFor(sources),
+            ...(overflow ? { overflow } : {}),
+        };
     },
     format: (result) => {
         const lines = [`## Structures (${result.structures.length})`];
@@ -239,6 +263,10 @@ export const getStructure = tool('protein_get_structure', {
             for (const s of result.overflow.sections)
                 lines.push(`- ${s.id}: ${s.bytes} bytes`);
         }
+        if (result.attribution.length > 0) {
+            lines.push(`\n### Attribution`);
+            lines.push(...renderAttribution(result.attribution));
+        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });

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

@@ -54,6 +54,7 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
                     label: z.ZodString;
                     count: z.ZodNumber;
                 }, z.core.$strip>>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
             }, z.core.$strip>>>;
         }, z.core.$strip>>;
         truncated: z.ZodOptional<z.ZodBoolean>;

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;AAwBjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0L3B,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;AAwBjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4L3B,CAAC"}

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

@@ -128,7 +128,9 @@ export const searchStructures = tool('protein_search_structures', {
     },
     async handler(input, ctx) {
         if (!input.query && !input.sequence && !input.organism) {
-            throw ctx.fail('no_criteria', 'Provide a query, sequence, or organism to search on.');
+            throw ctx.fail('no_criteria', 'Provide a query, sequence, or organism to search on.', {
+                ...ctx.recoveryFor('no_criteria'),
+            });
         }
         const cfg = getServerConfig();
         const rcsb = getRcsbService();

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.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,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkLvB,CAAC"}
+{"version":3,"file":"track-ligands.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/track-ligands.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,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiMvB,CAAC"}

package/dist/mcp-server/tools/definitions/track-ligands.tool.js

@@ -116,7 +116,9 @@ export const trackLigands = tool('protein_track_ligands', {
         const cfg = getServerConfig();
         if (input.mode === 'find_ligand') {
             if (!input.query)
-                throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".');
+                throw ctx.fail('missing_param', 'mode find_ligand requires a name or formula in "query".', {
+                    ...ctx.recoveryFor('missing_param'),
+                });
             const ids = await rcsb.findChemComps(input.query, input.limit, ctx);
             const ligands = (await mapWithConcurrency(ids, cfg.fanoutConcurrency, (id) => rcsb.getChemComp(id, ctx))).filter((c) => c != null);
             if (ligands.length === 0) {
@@ -131,7 +133,9 @@ export const trackLigands = tool('protein_track_ligands', {
         if (input.mode === 'structures_with_ligand') {
             const compId = input.comp_id?.toUpperCase();
             if (!compId)
-                throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".');
+                throw ctx.fail('missing_param', 'mode structures_with_ligand requires a "comp_id".', {
+                    ...ctx.recoveryFor('missing_param'),
+                });
             const result = await rcsb.searchByLigand(compId, { limit: input.limit }, ctx);
             ctx.enrich.total(result.total);
             ctx.enrich({ resolvedCompId: compId });
@@ -148,7 +152,9 @@ export const trackLigands = tool('protein_track_ligands', {
         // binding_site
         const compId = input.comp_id?.toUpperCase();
         if (!input.pdb_id)
-            throw ctx.fail('missing_param', 'mode binding_site requires a "pdb_id".');
+            throw ctx.fail('missing_param', 'mode binding_site requires a "pdb_id".', {
+                ...ctx.recoveryFor('missing_param'),
+            });
         const sites = await rcsb.getBindingSites(input.pdb_id, compId, ctx);
         if (sites.length === 0) {
             throw ctx.fail('not_found', `No binding-site contacts found in ${input.pdb_id.toUpperCase()}${compId ? ` for ligand ${compId}` : ''}.`, {
@@ -157,9 +163,15 @@ export const trackLigands = tool('protein_track_ligands', {
                 },
             });
         }
+        // Cap binding-site INSTANCES to the shared limit (mode-consistent top-N; the
+        // other two modes already bound their results). Disclose the drop via notice.
+        const bindingSites = sites.slice(0, input.limit);
+        if (sites.length > input.limit) {
+            ctx.enrich.notice(`Showing ${input.limit} of ${sites.length} binding-site instances in ${input.pdb_id.toUpperCase()}${compId ? ` for ${compId}` : ''}; raise limit to see more.`);
+        }
         if (compId)
             ctx.enrich({ resolvedCompId: compId });
-        return { mode: input.mode, bindingSites: sites };
+        return { mode: input.mode, bindingSites };
     },
     format: (result) => {
         const lines = [`## protein_track_ligands — ${result.mode}`];