@cyanheads/protein-mcp-server 0.8.3 → 0.8.5

package/AGENTS.md

@@ -1,7 +1,7 @@
 # Developer Protocol
 
 **Server:** protein-mcp-server
-**Version:** 0.8.3
+**Version:** 0.8.5
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
 **Engines:** Bun ≥1.4.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Developer Protocol
 
 **Server:** protein-mcp-server
-**Version:** 0.8.3
+**Version:** 0.8.5
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
 **Engines:** Bun ≥1.4.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0

package/README.md

@@ -7,7 +7,7 @@
 
 <div align="center">
 
-[![Version](https://img.shields.io/badge/Version-0.8.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.8.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)
 
 </div>
 
@@ -82,7 +82,9 @@ All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `pr
 - Both modes accept `start`/`limit` and report `totalCount`, echoing `start` and returning `nextStart` while another page remains; an empty page past the end names the offset in `notice`, distinct from a search with no matches
 - Foldseek targets default to `pdb100` + `afdb50`; override via `databases` (e.g. `afdb-swissprot`, `BFVD`)
 - An async job that exceeds the poll budget returns `status: computing` with a `ticketId` — re-call with `ticket_id` to resume; a completed structure search returns the same ticket so a new `start` pages the finished job
-- Each mode reads only its own controls (`sequence`, `max_evalue`, `min_identity` under `by: sequence`; `ticket_id`, `databases` under `by: structure`) — a field the selected mode can't consume is rejected, not ignored
+- Foldseek searches each chain of a multichain structure as its own query: a structure response covers one query (`query`, 0-based, default `0`) and reports `queryCount`, with a `notice` naming the other queries; pass `query` with `ticket_id` to read another chain's hits from the same job. An out-of-range `query` is rejected (`query_out_of_range`), not answered with an empty list
+- Structure hits are ranked best first by `score` across every searched database (hits without a score last, ties by database then target) before `start`/`limit` paging
+- Each mode reads only its own controls (`sequence`, `max_evalue`, `min_identity` under `by: sequence`; `ticket_id`, `databases`, `query` under `by: structure`) — a field the selected mode can't consume is rejected, not ignored
 - Each hit names the engine and source database it came from
 
 ---
@@ -90,9 +92,11 @@ All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `pr
 ### `protein_track_ligands` <sub>tool</sub>
 
 - `mode: find_ligand` resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey — ranked by deposition frequency, most-common match first
+- `totalCount` and `candidatesConsidered` report how many components matched and how many were ranked; a broad name whose matches exceed the candidate pool gets a `notice` to narrow the query
 - A formula-shaped `query` matches on exact composition, spaced (`C29 H31 N7 O`) or unspaced; anything else (a component ID included) matches on name and synonyms
 - `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID, with `start`/`limit` paging and `nextStart` while another page remains; a page past the end names the offset in `notice` instead of reporting no entries
-- `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances
+- `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances; ligand instances page with `start`/`limit` like `structures_with_ligand`
+- Pocket residues carry both mmCIF label numbering (`asymId`, `seqId`) and author numbering (`authAsymId`, `authSeqId`) — 1IEP's imatinib pocket lists label THR93 as author THR315; the ligand instance reports its own author chain and residue number
 - Binding sites are experimental-only — computed from deposited coordinates; predicted models carry no bound ligands
 
 ---

package/changelog/0.8.x/0.8.4.md

@@ -0,0 +1,13 @@
+---
+summary: "Fixes protein_find_similar by:structure exposing only Foldseek's first chain query and ranking hits per-database instead of by combined score."
+breaking: false
+security: false
+---
+
+# 0.8.4 — 2026-09-22
+
+## Fixed
+
+- **`protein_find_similar` `by: "structure"`** — a multichain structure's Foldseek job now exposes every chain's query instead of always reading query 0: a new `query` input (0-based, default 0) selects one, the response reports `query`/`queryCount`, and an out-of-range index is rejected with a typed `query_out_of_range` error rather than the provider's silent empty result (#63).
+- **`protein_find_similar` `by: "structure"`** — hits are now ranked by `score` across every searched database before `start`/`limit` paging, instead of the previous per-database block order that could bury a stronger hit from a later database behind weaker hits from the first (#64).
+- **`FoldseekService.parseTarget`** — PDB target headers in assembly form (`1crn-assembly1.cif.gz_A`) now resolve the chain letter; previously only bare (`1abc_A`) headers parsed.

package/changelog/0.8.x/0.8.5.md

@@ -0,0 +1,16 @@
+---
+summary: "protein_track_ligands find_ligand reports candidate-pool totals, binding_site adds author residue numbering and pages ligand instances."
+breaking: false
+security: false
+---
+
+# 0.8.5 — 2026-09-22
+
+## Added
+
+- **`protein_track_ligands` `binding_site`** — pocket residues now carry author numbering (`authAsymId`/`authSeqId`) beside the mmCIF label numbering (`asymId`/`seqId`), and the ligand instance adds its author residue number (`ligandAuthSeqId`). The author chain comes from the entry's per-instance label/author chain pairs; field descriptions and the rendered text name each namespace, including `ligandAsymId` as an author chain ID (#69).
+
+## Fixed
+
+- **`protein_track_ligands` `find_ligand`** — responses now report `totalCount` (the upstream match total) and `candidatesConsidered` (the components pulled into the deposition-frequency ranking), with a `notice` to narrow the query when a broad name's matches exceed that pool; previously the total was discarded and the truncation went undisclosed (#67).
+- **`protein_track_ligands` `binding_site`** — ligand instances now page with `start`/`limit`, reporting `totalCount`/`start`/`nextStart`, naming the next `start` in the notice, and giving a past-end `start` its own notice; previously `start` was ignored in this mode and the notice pointed at a `limit` above its 100 cap, so instances past the first 100 were unreachable (#75).

package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts

@@ -5,8 +5,9 @@
  * poll → bounded timeout, returning "still computing" rather than blocking).
  * Both modes page their results the same way (totalCount / start / nextStart),
  * and a completed structure job returns its ticket so it can be re-paged instead
- * of resubmitted. Fields the selected mode cannot consume are rejected, not
- * ignored.
+ * of resubmitted. A structure response covers one Foldseek query (one chain of a
+ * multichain file), selected by `query` and disclosed with `queryCount`. Fields
+ * the selected mode cannot consume are rejected, not ignored.
  * @module mcp-server/tools/definitions/find-similar.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -21,6 +22,7 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     uniprot: z.ZodOptional<z.ZodString>;
     ticket_id: z.ZodOptional<z.ZodString>;
     databases: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    query: z.ZodOptional<z.ZodNumber>;
     max_evalue: z.ZodOptional<z.ZodNumber>;
     min_identity: z.ZodOptional<z.ZodNumber>;
     limit: z.ZodDefault<z.ZodNumber>;
@@ -36,6 +38,8 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
         computing: "computing";
     }>;
     ticketId: z.ZodOptional<z.ZodString>;
+    query: z.ZodOptional<z.ZodNumber>;
+    queryCount: z.ZodOptional<z.ZodNumber>;
     hits: z.ZodArray<z.ZodObject<{
         id: z.ZodString;
         entityId: z.ZodOptional<z.ZodString>;
@@ -60,8 +64,8 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
 }, {
     readonly reason: "mode_mismatched_field";
     readonly code: JsonRpcErrorCode.InvalidParams;
-    readonly when: "An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:\"structure\"; ticket_id or a non-empty databases list under by:\"sequence\".";
-    readonly recovery: "Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:\"sequence\"; ticket_id and databases apply to by:\"structure\".";
+    readonly when: "An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:\"structure\"; ticket_id, query or a non-empty databases list under by:\"sequence\".";
+    readonly recovery: "Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:\"sequence\"; ticket_id, databases and query apply to by:\"structure\".";
     readonly thrownBy: "service";
 }, {
     readonly reason: "no_sequence";
@@ -69,6 +73,12 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     readonly when: "A sequence could not be resolved from the given PDB ID or UniProt accession.";
     readonly recovery: "Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.";
     readonly thrownBy: "service";
+}, {
+    readonly reason: "query_out_of_range";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "The requested query index is not below the number of queries the completed Foldseek job holds.";
+    readonly recovery: "Re-call with the ticket_id from the error and a query index below the reported query count; the job is already complete.";
+    readonly thrownBy: "service";
 }, {
     readonly reason: "search_failed";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;

package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsFtB,CAAC"}
+{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4JjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkGtB,CAAC"}

package/dist/mcp-server/tools/definitions/find-similar.tool.js

@@ -5,8 +5,9 @@
  * poll → bounded timeout, returning "still computing" rather than blocking).
  * Both modes page their results the same way (totalCount / start / nextStart),
  * and a completed structure job returns its ticket so it can be re-paged instead
- * of resubmitted. Fields the selected mode cannot consume are rejected, not
- * ignored.
+ * of resubmitted. A structure response covers one Foldseek query (one chain of a
+ * multichain file), selected by `query` and disclosed with `queryCount`. Fields
+ * the selected mode cannot consume are rejected, not ignored.
  * @module mcp-server/tools/definitions/find-similar.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -38,6 +39,12 @@ const inputSchema = z.object({
         .array(z.string())
         .optional()
         .describe('Foldseek target databases (by:structure). Default pdb100 + afdb50. e.g. afdb-swissprot, BFVD.'),
+    query: z
+        .number()
+        .int()
+        .min(0)
+        .optional()
+        .describe('Zero-based Foldseek query index (by:structure). Default 0. Foldseek splits a multichain structure into one query per chain, in file order; queryCount in the response says how many the job holds. Pass the same value with ticket_id to resume or re-page that query.'),
     max_evalue: z
         .number()
         .positive()
@@ -67,6 +74,14 @@ const outputSchema = z.object({
         .string()
         .optional()
         .describe('Async job ticket ID (by:structure). Present while status is computing, and also on a complete response — re-call with ticket_id plus a different start/limit to page the same finished job instead of resubmitting.'),
+    query: z
+        .number()
+        .optional()
+        .describe('Zero-based Foldseek query index the hits belong to (by:structure).'),
+    queryCount: z
+        .number()
+        .optional()
+        .describe('Number of queries the Foldseek job holds, one per chain of the submitted structure (by:structure, complete). Valid query values run from 0 to queryCount - 1.'),
     hits: z
         .array(z
         .object({
@@ -98,7 +113,7 @@ const outputSchema = z.object({
             .describe('UniProt accession (predicted structure hits).'),
     })
         .describe('A similar protein, with alignment scores when available.'))
-        .describe('Similar proteins, best first.'),
+        .describe('Similar proteins, best first. Structure hits are ranked by score across all searched databases (hits without a score last, ties by database then target).'),
 });
 const enrichmentShape = {
     totalCount: z.number().optional().describe('Total upstream matches before pagination.'),
@@ -110,11 +125,11 @@ const enrichmentShape = {
     notice: z
         .string()
         .optional()
-        .describe('Advisory note: a structure job still computing (with how to resume it), no matches, or a start past the end of the results.'),
+        .describe('Advisory note: a structure job still computing (with how to resume it), no matches, a start past the end of the results, or other queries in a multichain structure job.'),
 };
 export const findSimilar = tool('protein_find_similar', {
     title: 'protein-mcp-server: find similar',
-    description: `Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against experimental and predicted databases; if the job is still computing when the poll budget elapses, the response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume the same job instead of resubmitting, and a complete response carries the same ticket so a finished job can be re-paged with a different start. Each mode reads only its own controls: sequence, max_evalue and min_identity belong to by:"sequence"; ticket_id and databases belong to by:"structure"; pdb_id, uniprot, start and limit are shared. A field the selected mode cannot consume is rejected rather than silently ignored. Output names the engine and database each hit came from.`,
+    description: `Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against experimental and predicted databases; if the job is still computing when the poll budget elapses, the response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume the same job instead of resubmitting, and a complete response carries the same ticket so a finished job can be re-paged with a different start. Foldseek searches each chain of a multichain structure as its own query: a response covers one query (query, default 0), reports queryCount, and ranks that query's hits by score across all searched databases. Each mode reads only its own controls: sequence, max_evalue and min_identity belong to by:"sequence"; ticket_id, databases and query belong to by:"structure"; pdb_id, uniprot, start and limit are shared. A field the selected mode cannot consume is rejected rather than silently ignored. Output names the engine and database each hit came from.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     // Every reason is thrown by a helper below the handler, hence thrownBy on each entry.
     errors: [
@@ -128,8 +143,8 @@ export const findSimilar = tool('protein_find_similar', {
         {
             reason: 'mode_mismatched_field',
             code: JsonRpcErrorCode.InvalidParams,
-            when: 'An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:"structure"; ticket_id or a non-empty databases list under by:"sequence".',
-            recovery: 'Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:"sequence"; ticket_id and databases apply to by:"structure".',
+            when: 'An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:"structure"; ticket_id, query or a non-empty databases list under by:"sequence".',
+            recovery: 'Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:"sequence"; ticket_id, databases and query apply to by:"structure".',
             thrownBy: 'service',
         },
         {
@@ -139,6 +154,13 @@ export const findSimilar = tool('protein_find_similar', {
             recovery: 'Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.',
             thrownBy: 'service',
         },
+        {
+            reason: 'query_out_of_range',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'The requested query index is not below the number of queries the completed Foldseek job holds.',
+            recovery: 'Re-call with the ticket_id from the error and a query index below the reported query count; the job is already complete.',
+            thrownBy: 'service',
+        },
         {
             reason: 'search_failed',
             code: JsonRpcErrorCode.ServiceUnavailable,
@@ -170,8 +192,12 @@ export const findSimilar = tool('protein_find_similar', {
     },
     format: (result) => {
         const lines = [`## ${result.engine} (by:${result.by}) — ${result.status}`];
-        if (result.ticketId)
-            lines.push(`**Ticket:** ${result.ticketId} — re-call with ticket_id to resume or re-page this job.`);
+        if (result.ticketId) {
+            const withQuery = result.query ? ` and query ${result.query}` : '';
+            lines.push(`**Ticket:** ${result.ticketId} — re-call with ticket_id${withQuery} to resume or re-page this job.`);
+        }
+        if (typeof result.queryCount === 'number')
+            lines.push(`**Query:** ${result.query ?? 0} of ${result.queryCount} (0-based)`);
         for (const h of result.hits) {
             lines.push(`\n### ${h.id} _(${h.source})_`);
             if (h.title)
@@ -241,12 +267,13 @@ async function runSequence(input, ctx) {
 }
 async function runStructure(input, timeoutMs, ctx) {
     const foldseek = getFoldseekService();
+    const query = input.query ?? 0;
     let outcome;
     if (input.ticket_id) {
         // Resume path: poll the existing ticket, skipping coordinate resolution +
         // submit. A completed ticket is idempotent upstream, so a re-call with a new
-        // start/limit pages the same finished job instead of running a second search.
-        outcome = await foldseek.resume({ ticketId: input.ticket_id, limit: input.limit, start: input.start, timeoutMs }, ctx);
+        // start/limit/query pages the same finished job instead of running a second search.
+        outcome = await foldseek.resume({ ticketId: input.ticket_id, query, limit: input.limit, start: input.start, timeoutMs }, ctx);
     }
     else {
         const { content, fileName } = await resolveCoordinateFile(input, ctx);
@@ -255,11 +282,22 @@ async function runStructure(input, timeoutMs, ctx) {
             fileName,
             databases: input.databases && input.databases.length > 0 ? input.databases : DEFAULT_FOLDSEEK_DBS,
             mode: FOLDSEEK_MODE,
+            query,
             limit: input.limit,
             start: input.start,
             timeoutMs,
         }, ctx);
     }
+    if (outcome.status === 'query_out_of_range') {
+        const { ticketId, queryCount } = outcome;
+        throw ctx.fail('query_out_of_range', `query ${query} is out of range: Foldseek ticket ${ticketId} holds ${queryCount} ${queryCount === 1 ? 'query' : 'queries'}.`, {
+            recovery: {
+                hint: queryCount > 0
+                    ? `Re-call with ticket_id "${ticketId}" and query between 0 and ${queryCount - 1}; the job is already complete, so nothing is resubmitted.`
+                    : 'Foldseek read no chains from the submitted structure; confirm it has protein coordinates via protein_get_structure.',
+            },
+        });
+    }
     if (outcome.status === 'not_found') {
         throw ctx.fail('ticket_not_found', `Foldseek ticket ${outcome.ticketId} is invalid or expired.`, { ...ctx.recoveryFor('ticket_not_found') });
     }
@@ -271,12 +309,14 @@ async function runStructure(input, timeoutMs, ctx) {
         });
     }
     if (outcome.status === 'computing') {
-        ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar with ticket_id set to "${outcome.ticketId}" to resume.`);
+        const withQuery = query > 0 ? ` and query ${query}` : '';
+        ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar with ticket_id set to "${outcome.ticketId}"${withQuery} to resume.`);
         return {
             by: 'structure',
             engine: 'Foldseek',
             status: 'computing',
             ticketId: outcome.ticketId,
+            query,
             hits: [],
         };
     }
@@ -291,17 +331,27 @@ async function runStructure(input, timeoutMs, ctx) {
     });
     // An empty page has two unrelated causes now that `start` pages a completed
     // job, and they need opposite next moves: no hits at all means widen the
-    // databases, while a start past the end means ask for a lower offset.
+    // databases, while a start past the end means ask for a lower offset. A
+    // multichain job adds a third note — this page covers one query of several.
+    // `notice` is last-wins, so the applicable notes are joined into one string.
+    const notes = [];
     if (outcome.hits.length === 0) {
-        ctx.enrich.notice(outcome.total === 0
+        notes.push(outcome.total === 0
             ? 'Foldseek returned no fold-similar hits in the selected databases.'
             : `start ${input.start} is past the end of this job's ${outcome.total} hits. Re-call with a lower start to read a populated page.`);
     }
+    if (outcome.queryCount > 1) {
+        notes.push(`This job holds ${outcome.queryCount} queries, one per chain Foldseek read from the submitted structure in file order; these hits are for query ${outcome.query}. Re-call with ticket_id "${outcome.ticketId}" and a different query (0–${outcome.queryCount - 1}) to read another chain's hits.`);
+    }
+    if (notes.length > 0)
+        ctx.enrich.notice(notes.join(' '));
     return {
         by: 'structure',
         engine: 'Foldseek',
         status: 'complete',
         ticketId: outcome.ticketId,
+        query: outcome.query,
+        queryCount: outcome.queryCount,
         hits: outcome.hits.map((h) => ({
             id: h.pdbId ?? h.uniprotAccession ?? h.target,
             source: h.targetType === 'alphafold' ? 'predicted' : 'experimental',
@@ -316,7 +366,7 @@ async function runStructure(input, timeoutMs, ctx) {
 /**
  * Reject an input field the selected `by` mode cannot consume. Each branch reads
  * only its own subset — `runSequence` alone reads sequence/max_evalue/
- * min_identity, `runStructure` alone reads ticket_id/databases — so a field
+ * min_identity, `runStructure` alone reads ticket_id/databases/query — so a field
  * supplied for the other mode would be dropped silently, making an unfiltered
  * search look filtered or an unscoped one look scoped. Guarded here rather than
  * by a Zod refine so the rejection carries `data.reason` and a recovery hint
@@ -334,6 +384,7 @@ function rejectModeMismatchedFields(input, ctx) {
         : [
             typeof input.ticket_id === 'string' ? 'ticket_id' : null,
             input.databases && input.databases.length > 0 ? 'databases' : null,
+            typeof input.query === 'number' ? 'query' : null,
         ]).filter((field) => field !== null);
     if (offenders.length === 0)
         return;

package/dist/mcp-server/tools/definitions/find-similar.tool.js.map

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

@@ -41,10 +41,13 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
     bindingSites: z.ZodOptional<z.ZodArray<z.ZodObject<{
         ligandCompId: z.ZodString;
         ligandAsymId: z.ZodOptional<z.ZodString>;
+        ligandAuthSeqId: z.ZodOptional<z.ZodNumber>;
         residues: z.ZodArray<z.ZodObject<{
             residueCompId: z.ZodString;
             asymId: z.ZodString;
             seqId: z.ZodOptional<z.ZodNumber>;
+            authAsymId: z.ZodOptional<z.ZodString>;
+            authSeqId: z.ZodOptional<z.ZodNumber>;
             distance: z.ZodOptional<z.ZodNumber>;
         }, z.core.$strip>>;
     }, z.core.$strip>>>;
@@ -60,6 +63,7 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
     readonly recovery: "Use mode \"find_ligand\" to resolve a name to a component ID first, then confirm the ligand is present in the structure via protein_get_structure.";
 }], {
     readonly totalCount: z.ZodOptional<z.ZodNumber>;
+    readonly candidatesConsidered: z.ZodOptional<z.ZodNumber>;
     readonly start: z.ZodOptional<z.ZodNumber>;
     readonly nextStart: z.ZodOptional<z.ZodNumber>;
     readonly resolvedCompId: z.ZodOptional<z.ZodString>;

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

@@ -1 +1 @@
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+{"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;AAwEjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4SvB,CAAC"}