npm - @cyanheads/protein-mcp-server - Versions diffs - 0.6.0 → 0.7.0 - Mend

@cyanheads/protein-mcp-server 0.6.0 → 0.7.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.6.0
+**Version:** 0.7.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.7`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.6.0
+**Version:** 0.7.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.7`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.6.0-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-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.7.0-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-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -62,7 +62,9 @@ Fetch structures with metadata and coordinate-file URLs, resolving across provid
 - `source: predicted` takes UniProt accessions and returns the AlphaFold model with pLDDT/PAE confidence
 - `source: best_available` takes UniProt accessions and returns the top federated model (experimental if one exists, else the best prediction)
 - Per-ID partial success — unresolved IDs are listed in `failed[]`, not a batch-level error
-- `include_coords` inlines coordinate content; when a batch overflows the response budget it returns a per-structure size outline, so you can re-call with `sections: [ids]` for specific structures
+- Batch cap disclosure — `requested` is the original request length and `processed` the count after the cap, so IDs dropped beyond the cap are visible rather than silently discarded; every advisory (cap, partial failure, coordinate overflow, failed inlining) is joined into one `notice`
+- Records served by the RCSB entry endpoint also carry `polymerEntities` (with both `authAsymIds` and `labelAsymIds`), `ligands`, `molecularWeight`, and `releaseDate`
+- `include_coords` inlines coordinate content, subject to the response budget: a batch over budget returns a per-structure size outline you can re-call with `sections: [ids]`, and a single file over budget is withheld with a pointer to its `coordinateUrls` (a `sections` re-call would return the same bytes). Withheld content never appears on either surface
 - Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
 ---
@@ -136,7 +138,7 @@ Sequence and functional annotation for a protein.
 | Type | Name | Description |
 |:---|:---|:---|
-| Resource | `pdb://{entry_id}` | Experimental structure summary for a PDB entry — title, method, resolution, organism, chains, and bound ligands. |
+| Resource | `pdb://{entry_id}` | Experimental structure summary for a PDB entry — title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (`authAsymIds`) and mmCIF label (`labelAsymIds`) namespaces. |
 | Resource | `af://{uniprot}` | Predicted-structure summary for a UniProt accession from AlphaFold DB — mean pLDDT, confidence-band fractions, model URLs, and version. |
 All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `protein_get_structure` for `source: experimental`, and `af://{uniprot}` mirrors it for `source: predicted`. Many MCP clients are tool-only and don't surface resources; the summaries remain reachable through the tools.

package/changelog/0.7.x/0.7.0.md ADDED Viewed

@@ -0,0 +1,25 @@
+---
+summary: "protein_get_structure exposes per-entity authAsymIds/labelAsymIds chain namespaces plus entry detail (ligands, molecular weight, release date), accumulates every advisory instead of overwriting, and gates the coordinate overflow budget on a single oversized file too; pdb://{entry_id}'s polymerEntities[].chains is renamed to authAsymIds."
+breaking: true
+security: false
+---
+# 0.7.0 — 2026-09-08
+## Added
+- **`protein_get_structure`** and **`pdb://{entry_id}`** expose per-polymer-entity `authAsymIds` (`auth_asym_id`) and `labelAsymIds` (`label_asym_id`) — the two chain namespaces are unrelated by any transformation and each feeds a different tool parameter ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+- **`protein_get_structure`** experimental records now also carry `polymerEntities`, `ligands`, `molecularWeight`, and `releaseDate`, matching `pdb://{entry_id}` for the same entry ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+- **`protein_get_structure`** enrichment gains a `processed` field — the ID count after the batch cap — alongside `requested` ([#43](https://github.com/cyanheads/protein-mcp-server/issues/43)).
+## Changed
+- **`pdb://{entry_id}`'s `polymerEntities[].chains`** is renamed to `authAsymIds`; `protein_get_annotations`' `chain` description and its `chain_not_found` recovery hint now point at `authAsymIds` ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+- **`protein_get_structure`'s `requested`** now reports the original `input.ids.length`, not the post-cap count — a call over the batch cap previously reported `requested` equal to the capped `processed` value ([#43](https://github.com/cyanheads/protein-mcp-server/issues/43)).
+- **`protein_compare_structures`'** `chain` description now names `label_asym_id` and points at `polymerEntities[].labelAsymIds`, distinguishing it from the author-chain namespace `protein_get_annotations.chain` takes ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+## Fixed
+- **`protein_get_structure`** no longer loses the batch-cap advisory when a partial failure or coordinate overflow follows it — every applicable advisory (cap, partial failure, overflow, failed inlining) now accumulates into one `notice` instead of the last write winning ([#43](https://github.com/cyanheads/protein-mcp-server/issues/43)).
+- **`protein_get_structure`'s coordinate-inlining budget** now also gates a single requested file — previously only a batch of 2+ triggered the overflow guard, so one oversized file (e.g. `4HHB.cif` at 772 KB) inlined whole on `structuredContent` while `format()` silently truncated it to a 2,000-byte prefix ([#42](https://github.com/cyanheads/protein-mcp-server/issues/42)).
+- **`protein_get_structure`** now names the structure ID when its coordinate fetch fails, instead of returning a response indistinguishable from one where coordinates were never requested ([#42](https://github.com/cyanheads/protein-mcp-server/issues/42)).

package/dist/mcp-server/resources/definitions/pdb-summary.resource.d.ts CHANGED Viewed

@@ -1,7 +1,8 @@
 /**
  * @fileoverview pdb://{entry_id} — experimental structure summary (title, method,
- * resolution, organism, ligands, chains). The injectable-context twin of
- * protein_get_structure for source: experimental.
+ * resolution, organism, ligands, and per-entity chain IDs in both the author and
+ * mmCIF label namespaces). The injectable-context twin of protein_get_structure
+ * for source: experimental.
  * @module mcp-server/resources/definitions/pdb-summary.resource
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -19,7 +20,8 @@ export declare const pdbSummaryResource: import("@cyanheads/mcp-ts-core").Resour
         entityId: z.ZodString;
         description: z.ZodOptional<z.ZodString>;
         organism: z.ZodOptional<z.ZodString>;
-        chains: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        authAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        labelAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
         sequenceLength: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     ligands: z.ZodArray<z.ZodObject<{

package/dist/mcp-server/resources/definitions/pdb-summary.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"pdb-summary.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/pdb-summary.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKrD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;6BA6C7B,CAAC"}

package/dist/mcp-server/resources/definitions/pdb-summary.resource.js CHANGED Viewed

@@ -1,16 +1,18 @@
 /**
  * @fileoverview pdb://{entry_id} — experimental structure summary (title, method,
- * resolution, organism, ligands, chains). The injectable-context twin of
- * protein_get_structure for source: experimental.
+ * resolution, organism, ligands, and per-entity chain IDs in both the author and
+ * mmCIF label namespaces). The injectable-context twin of protein_get_structure
+ * for source: experimental.
  * @module mcp-server/resources/definitions/pdb-summary.resource
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
 import { notFound } from '@cyanheads/mcp-ts-core/errors';
+import { ligandSchema, polymerEntitySchema } from '../../tools/definitions/_schemas.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
 export const pdbSummaryResource = resource('pdb://{entry_id}', {
     name: 'pdb-structure-summary',
     title: 'PDB structure summary',
-    description: 'Experimental structure summary for a PDB entry: title, method, resolution, organism, chains, and bound ligands.',
+    description: 'Experimental structure summary for a PDB entry: title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (auth_asym_id) and mmCIF label (label_asym_id) namespaces.',
     mimeType: 'application/json',
     params: z.object({
         entry_id: z.string().describe('PDB entry ID (e.g. 4HHB).'),
@@ -24,25 +26,9 @@ export const pdbSummaryResource = resource('pdb://{entry_id}', {
         releaseDate: z.string().optional().describe('Initial release date (ISO 8601).'),
         organisms: z.array(z.string()).describe('Source organisms.'),
         polymerEntities: z
-            .array(z
-            .object({
-            entityId: z.string().describe('Polymer entity ID.'),
-            description: z.string().optional().describe('Entity description.'),
-            organism: z.string().optional().describe('Source organism.'),
-            chains: z.array(z.string()).optional().describe('Author chain IDs.'),
-            sequenceLength: z.number().optional().describe('Residue count.'),
-        })
-            .describe('A modeled polymer entity (chain group).'))
-            .describe('Modeled polymer entities.'),
-        ligands: z
-            .array(z
-            .object({
-            compId: z.string().describe('Chemical component ID.'),
-            name: z.string().optional().describe('Chemical name.'),
-            formula: z.string().optional().describe('Molecular formula.'),
-        })
-            .describe('A bound ligand (non-polymer chemical component).'))
-            .describe('Bound ligands.'),
+            .array(polymerEntitySchema)
+            .describe('Modeled polymer entities, each carrying both chain namespaces — authAsymIds for protein_get_annotations, labelAsymIds for protein_compare_structures.'),
+        ligands: z.array(ligandSchema).describe('Bound ligands.'),
     }),
     async handler(params, ctx) {
         const [meta] = await getRcsbService().getEntries([params.entry_id], ctx);

package/dist/mcp-server/resources/definitions/pdb-summary.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"pdb-summary.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/pdb-summary.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,YAAY,EAAE,mBAAmB,EAAE,MAAM,4CAA4C,CAAC;AAC/F,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,kBAAkB,EAAE;IAC7D,IAAI,EAAE,uBAAuB;IAC7B,KAAK,EAAE,uBAAuB;IAC9B,WAAW,EACT,4MAA4M;IAC9M,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;KAC3D,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;QACxC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACzD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;QAC3E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QAC9D,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACpF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/E,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAC5D,eAAe,EAAE,CAAC;aACf,KAAK,CAAC,mBAAmB,CAAC;aAC1B,QAAQ,CACP,uJAAuJ,CACxJ;QACH,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,gBAAgB,CAAC;KAC1D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,MAAM,CAAC,IAAI,CAAC,GAAG,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,GAAG,CAAC,CAAC;QACzE,IAAI,CAAC,IAAI;YACP,MAAM,QAAQ,CAAC,0BAA0B,MAAM,CAAC,QAAQ,CAAC,WAAW,EAAE,EAAE,EAAE;gBACxE,OAAO,EAAE,MAAM,CAAC,QAAQ;aACzB,CAAC,CAAC;QACL,OAAO;YACL,EAAE,EAAE,IAAI,CAAC,EAAE;YACX,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC5C,GAAG,CAAC,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7E,GAAG,CAAC,OAAO,IAAI,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,OAAO,IAAI,CAAC,eAAe,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,eAAe,EAAE,IAAI,CAAC,eAAe,EAAE;gBAC3C,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC9D,SAAS,EAAE,IAAI,CAAC,SAAS;YACzB,eAAe,EAAE,IAAI,CAAC,eAAe;YACrC,OAAO,EAAE,IAAI,CAAC,OAAO;SACtB,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/_schemas.d.ts CHANGED Viewed

@@ -6,7 +6,9 @@
  * cross-tab the facet engine produces; the flat variant drops the child position
  * for the tool that requests single-dimension breakdowns only. Every dimension
  * position also reports its coverage gap, so buckets that sum to less than the
- * stated total say so.
+ * stated total say so. Also holds the entry-level polymer-entity and ligand
+ * schemas shared by `protein_get_structure` and the `pdb://{entry_id}` resource,
+ * so tool and resource representations of the same record stay identical.
  * @module mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -116,4 +118,26 @@ export declare const attributionSchema: z.ZodObject<{
 export type AttributionOutput = z.infer<typeof attributionSchema>;
 /** Render an attribution list to one compact markdown line per source for `format()` parity. */
 export declare function renderAttribution(attributions: AttributionOutput[]): string[];
+/**
+ * One modeled polymer entity (chain group) of a PDB entry. Shared by
+ * `protein_get_structure` and the `pdb://{entry_id}` resource so the tool and its
+ * resource twin cannot drift on how the two chain namespaces are named or
+ * described. The `label_asym_id` / `auth_asym_id` split is load-bearing: the two
+ * are unrelated by any transformation, and each is consumed by a different tool
+ * parameter, so a caller that substitutes one for the other gets no alignment.
+ */
+export declare const polymerEntitySchema: z.ZodObject<{
+    entityId: z.ZodString;
+    description: z.ZodOptional<z.ZodString>;
+    organism: z.ZodOptional<z.ZodString>;
+    authAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    labelAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    sequenceLength: z.ZodOptional<z.ZodNumber>;
+}, z.core.$strip>;
+/** One bound non-polymer component (ligand) of a PDB entry. */
+export declare const ligandSchema: z.ZodObject<{
+    compId: z.ZodString;
+    name: z.ZodOptional<z.ZodString>;
+    formula: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>;
 //# sourceMappingURL=_schemas.d.ts.map

package/dist/mcp-server/tools/definitions/_schemas.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA~~;;;;;;;;;;GAUG~~;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAe,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAE5E;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;CAIuC,CAAC;AAkDxE;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;iBAgBwB,CAAC;AAE9D,qFAAqF;AACrF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;iBAI0D,CAAC;AAE5F,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,MAAM,MAAM,wBAAwB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,wBAAwB,CAAC,CAAC;AAgChF;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,KAAK,EAAE,cAAc,EACrB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,GACZ,oBAAoB,CAwBtB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,CAOnE;AA0CD,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAoBrE;AAuDD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAcvF;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CA8BvF;AAED,sFAAsF;AACtF,eAAO,MAAM,iBAAiB;;;;;iBAWmD,CAAC;AAElF,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAElE,gGAAgG;AAChG,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,EAAE,CAM7E"}
1	+ {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAe,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAE5E;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;CAIuC,CAAC;AAkDxE;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;iBAgBwB,CAAC;AAE9D,qFAAqF;AACrF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;iBAI0D,CAAC;AAE5F,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,MAAM,MAAM,wBAAwB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,wBAAwB,CAAC,CAAC;AAgChF;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,KAAK,EAAE,cAAc,EACrB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,GACZ,oBAAoB,CAwBtB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,CAOnE;AA0CD,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAoBrE;AAuDD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAcvF;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CA8BvF;AAED,sFAAsF;AACtF,eAAO,MAAM,iBAAiB;;;;;iBAWmD,CAAC;AAElF,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAElE,gGAAgG;AAChG,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,EAAE,CAM7E;AAED;;;;;;;GAOG;AACH,eAAO,MAAM,mBAAmB;;;;;;;iBAmBkD,CAAC;AAEnF,+DAA+D;AAC/D,eAAO,MAAM,YAAY;;;;iBAMsC,CAAC"}

package/dist/mcp-server/tools/definitions/_schemas.js CHANGED Viewed

@@ -6,7 +6,9 @@
  * cross-tab the facet engine produces; the flat variant drops the child position
  * for the tool that requests single-dimension breakdowns only. Every dimension
  * position also reports its coverage gap, so buckets that sum to less than the
- * stated total say so.
+ * stated total say so. Also holds the entry-level polymer-entity and ligand
+ * schemas shared by `protein_get_structure` and the `pdb://{entry_id}` resource,
+ * so tool and resource representations of the same record stay identical.
  * @module mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -343,4 +345,36 @@ export function renderAttribution(attributions) {
     }
     return lines;
 }
+/**
+ * One modeled polymer entity (chain group) of a PDB entry. Shared by
+ * `protein_get_structure` and the `pdb://{entry_id}` resource so the tool and its
+ * resource twin cannot drift on how the two chain namespaces are named or
+ * described. The `label_asym_id` / `auth_asym_id` split is load-bearing: the two
+ * are unrelated by any transformation, and each is consumed by a different tool
+ * parameter, so a caller that substitutes one for the other gets no alignment.
+ */
+export const polymerEntitySchema = z
+    .object({
+    entityId: z.string().describe('Polymer entity ID (e.g. 4HHB_1).'),
+    description: z.string().optional().describe('Entity description.'),
+    organism: z.string().optional().describe('Source organism.'),
+    authAsymIds: z
+        .array(z.string())
+        .optional()
+        .describe('Author-assigned chain IDs (auth_asym_id, e.g. ["A","C"]) — the namespace protein_get_annotations.chain takes. Omitted when upstream does not report them.'),
+    labelAsymIds: z
+        .array(z.string())
+        .optional()
+        .describe('mmCIF label_asym_id chain IDs (e.g. ["I","OB"]) — the namespace protein_compare_structures.chain takes. Not derivable from authAsymIds: for 6QNR_9 the label chains are I/OB against author chains 82/8E. Omitted when upstream does not report them.'),
+    sequenceLength: z.number().optional().describe('Residue count of the sample sequence.'),
+})
+    .describe('A modeled polymer entity (chain group), with both chain namespaces.');
+/** One bound non-polymer component (ligand) of a PDB entry. */
+export const ligandSchema = z
+    .object({
+    compId: z.string().describe('Chemical component ID (e.g. HEM).'),
+    name: z.string().optional().describe('Chemical name.'),
+    formula: z.string().optional().describe('Molecular formula.'),
+})
+    .describe('A bound ligand (non-polymer chemical component).');
 //# sourceMappingURL=_schemas.js.map

package/dist/mcp-server/tools/definitions/_schemas.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAsHjE~~,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmK5B,CAAC"}
1	+ {"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmK5B,CAAC"}

package/dist/mcp-server/tools/definitions/compare-structures.tool.js CHANGED Viewed

@@ -18,7 +18,7 @@ const inputSchema = z.object({
         chain: z
             .string()
             .optional()
-            .describe('Chain (label_asym_id) to restrict the alignment to a single chain.'),
+            .describe(`mmCIF label_asym_id restricting the alignment to a single chain. Read it from polymerEntities[].labelAsymIds on protein_get_structure (source experimental) or the pdb://{entry_id} resource. Author chain IDs are a different namespace — polymerEntities[].authAsymIds, what protein_get_annotations.chain takes — and are not interchangeable with this one. Case-sensitive.`),
     })
         .describe('A structure to align, by PDB entry ID with optional chain.'))
         .min(2)

package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts CHANGED Viewed

@@ -72,7 +72,7 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly reason: "chain_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.";
-    readonly 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).";
+    readonly recovery: "Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].authAsymIds in the pdb://{entry_id} resource).";
 }], {
     readonly resolvedFrom: z.ZodOptional<z.ZodString>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;

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

@@ -82,7 +82,7 @@ export const getAnnotations = tool('protein_get_annotations', {
             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).',
+            recovery: 'Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].authAsymIds in the pdb://{entry_id} resource).',
         },
     ],
     input: z.object({
@@ -97,7 +97,7 @@ export const getAnnotations = tool('protein_get_annotations', {
         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.'),
+            .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[].authAsymIds in the pdb://{entry_id} resource for an entry\'s author chain IDs.'),
         include: z
             .enum(['features', 'domains', 'variants', 'all'])
             .default('all')

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts CHANGED Viewed

@@ -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 { z } from '@cyanheads/mcp-ts-core';
@@ -30,6 +33,21 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
         method: z.ZodOptional<z.ZodString>;
         resolution: z.ZodOptional<z.ZodNumber>;
         organism: z.ZodOptional<z.ZodString>;
+        molecularWeight: z.ZodOptional<z.ZodNumber>;
+        releaseDate: z.ZodOptional<z.ZodString>;
+        polymerEntities: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            entityId: z.ZodString;
+            description: z.ZodOptional<z.ZodString>;
+            organism: z.ZodOptional<z.ZodString>;
+            authAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+            labelAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+            sequenceLength: z.ZodOptional<z.ZodNumber>;
+        }, z.core.$strip>>>;
+        ligands: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            compId: z.ZodString;
+            name: z.ZodOptional<z.ZodString>;
+            formula: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>>;
         provider: z.ZodOptional<z.ZodString>;
         confidence: z.ZodOptional<z.ZodNumber>;
         confidenceType: z.ZodOptional<z.ZodString>;
@@ -82,6 +100,7 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
     readonly recovery: "Verify ID formats (PDB IDs are 4 chars; UniProt accessions match the standard pattern) or locate IDs via protein_search_structures.";
 }], {
     readonly requested: z.ZodNumber;
+    readonly processed: z.ZodNumber;
     readonly resolved: z.ZodNumber;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8GjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6TvB,CAAC"}

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

@@ -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;
 }
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package/dist/mcp-server/tools/definitions/get-structure.tool.js.map CHANGED Viewed

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package/dist/services/rcsb/rcsb-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/rcsb/rcsb-service.js CHANGED Viewed

@@ -443,14 +443,21 @@ function normalizeEntry(raw) {
 }
 function normalizePolymerEntity(raw) {
     const organism = raw.rcsb_entity_source_organism?.find((o) => o.ncbi_scientific_name)?.ncbi_scientific_name;
-    const chains = raw.rcsb_polymer_entity_container_identifiers?.auth_asym_ids;
+    // Two distinct chain namespaces, never interchangeable: `auth_asym_ids` are the
+    // depositor's labels (what protein_get_annotations.chain takes), `asym_ids` the
+    // mmCIF label_asym_ids (what protein_compare_structures.chain takes). For many
+    // entries they coincide; for 6QNR_9 they are ["82","8E"] vs ["I","OB"].
+    const container = raw.rcsb_polymer_entity_container_identifiers;
+    const authAsymIds = container?.auth_asym_ids;
+    const labelAsymIds = container?.asym_ids;
     return {
         entityId: raw.rcsb_id ?? '',
+        ...(authAsymIds && authAsymIds.length > 0 ? { authAsymIds } : {}),
         ...(raw.rcsb_polymer_entity?.pdbx_description
             ? { description: raw.rcsb_polymer_entity.pdbx_description }
             : {}),
+        ...(labelAsymIds && labelAsymIds.length > 0 ? { labelAsymIds } : {}),
         ...(organism ? { organism } : {}),
-        ...(chains && chains.length > 0 ? { chains } : {}),
         ...(typeof raw.entity_poly?.rcsb_sample_sequence_length === 'number'
             ? { sequenceLength: raw.entity_poly.rcsb_sample_sequence_length }
             : {}),
@@ -509,7 +516,7 @@ const ENTRIES_QUERY = `query Entries($ids: [String!]!) {
     polymer_entities {
       rcsb_id
       rcsb_polymer_entity { pdbx_description }
-      rcsb_polymer_entity_container_identifiers { auth_asym_ids }
+      rcsb_polymer_entity_container_identifiers { auth_asym_ids asym_ids }
       entity_poly { rcsb_sample_sequence_length }
       rcsb_entity_source_organism { ncbi_scientific_name }
     }

package/dist/services/rcsb/rcsb-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/rcsb/types.d.ts CHANGED Viewed

@@ -61,12 +61,21 @@ export interface SearchResult {
 }
 /** A modeled polymer (protein/nucleic) entity within an entry. */
 export interface PolymerEntityMeta {
-    /** Author-assigned chain IDs for this entity. */
-    chains?: string[];
+    /**
+     * Author-assigned chain IDs (`auth_asym_id`) for this entity — the namespace
+     * `protein_get_annotations.chain` consumes. Absent when upstream omits it.
+     */
+    authAsymIds?: string[];
     /** Free-text description (e.g. "Hemoglobin subunit alpha"). */
     description?: string;
     /** Entity identifier (e.g. `4HHB_1`). */
     entityId: string;
+    /**
+     * mmCIF `label_asym_id` chain IDs for this entity — the namespace
+     * `protein_compare_structures.chain` consumes. Unrelated to `authAsymIds` by any
+     * transformation, though the two coincide for many entries.
+     */
+    labelAsymIds?: string[];
     /** Source organism scientific name. */
     organism?: string;
     /** One-letter canonical sequence (present only when explicitly requested). */

package/dist/services/rcsb/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.6.0",
+  "version": "0.7.0",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.6.0",
+  "version": "0.7.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.6.0",
+      "version": "0.7.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.6.0",
+      "version": "0.7.0",
       "packageArguments": [
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           "type": "positional",