npm - @cyanheads/protein-mcp-server - Versions diffs - 0.8.2 → 0.8.3 - Mend

@cyanheads/protein-mcp-server 0.8.2 → 0.8.3

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 (45) hide show

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

@@ -107,7 +107,10 @@ const enrichmentShape = {
         .number()
         .optional()
         .describe('Offset for the next result page; absent on the final or past-end page.'),
-    notice: z.string().optional().describe('Advisory note (still computing, empty results).'),
+    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.'),
 };
 export const findSimilar = tool('protein_find_similar', {
     title: 'protein-mcp-server: find similar',
@@ -209,8 +212,12 @@ async function runSequence(input, ctx) {
         start: input.start,
         ...(nextStart < result.total ? { nextStart } : {}),
     });
+    // Same two empty-page causes runStructure separates: nothing matched, or an
+    // offset past the end of a populated result set.
     if (result.hits.length === 0)
-        ctx.enrich.notice('No sequence-similar entries found. Lower min_identity or raise max_evalue.');
+        ctx.enrich.notice(result.total === 0
+            ? 'No sequence-similar entries found. Lower min_identity or raise max_evalue.'
+            : `start ${input.start} is past the end of the ${result.total} matches. Re-call with a lower start to read a populated page.`);
     return {
         by: 'sequence',
         engine: 'RCSB mmseqs2',
@@ -358,13 +365,14 @@ async function resolveSequence(input, ctx) {
         ...ctx.recoveryFor('missing_query'),
     });
 }
-/** Resolve a query coordinate file (PDB-format text) from a PDB ID or UniProt accession. */
+/** Resolve a query coordinate file (mmCIF or PDB-format text) from a PDB ID or UniProt accession. */
 async function resolveCoordinateFile(input, ctx) {
-    const rcsb = getRcsbService();
     if (input.pdb_id && isPdbId(input.pdb_id)) {
+        // mmCIF, not PDB format: every entry has an mmCIF file, while large entries
+        // are archived without a PDB-format one, and Foldseek reads either.
         const id = input.pdb_id.toUpperCase();
-        const content = await fetchCoordinateText(rcsb.coordinateFileUrl(id, 'pdb'), ctx);
-        return { content, fileName: `${id}.pdb` };
+        const content = await fetchCoordinateText(getRcsbService().mmcifUrl(id), ctx);
+        return { content, fileName: `${id}.cif` };
     }
     if (input.uniprot && isUniProtAccession(input.uniprot)) {
         const model = await getAlphaFoldService().getPrediction(input.uniprot, ctx);

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

	@@ -1 +1 @@
1	- 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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;AAoHjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsUvB,CAAC"}

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

@@ -14,7 +14,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { DEFAULT_OUTLINE_BUDGET_BYTES } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../../config/server-config.js';
-import { getAlphaFoldService } from '../../../services/alphafold/alphafold-service.js';
+import { getAlphaFoldService, } from '../../../services/alphafold/alphafold-service.js';
 import { getBeaconsService } from '../../../services/beacons/beacons-service.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
 import { mapWithConcurrency } from '../../../services/shared/async.js';
@@ -37,7 +37,7 @@ const structureRecordSchema = z
     pdbId: z
         .string()
         .optional()
-        .describe('Chosen PDB entry ID when a best_available query resolved to an experimental structure (id stays the queried UniProt accession). Lets an agent cite the structure without parsing the coordinate URL.'),
+        .describe('Chosen PDB entry ID when a best_available query resolved to an experimental structure (id stays the queried UniProt accession), so the structure can be cited without parsing the coordinate URL.'),
     title: z.string().optional().describe('Structure / protein title.'),
     method: z.string().optional().describe('Experimental method(s).'),
     resolution: z.number().optional().describe('Resolution in Å (experimental).'),
@@ -45,19 +45,19 @@ const structureRecordSchema = z
     molecularWeight: z
         .number()
         .optional()
-        .describe('Deposited structure molecular weight in kDa, from the RCSB entry record. Omitted when the record does not report one.'),
+        .describe('Deposited structure molecular weight in kDa. Present only when the call used source experimental; 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.'),
+        .describe('Initial release date (ISO 8601). Present only when the call used source experimental; 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.'),
+        .describe('Modeled polymer entities, each with both chain namespaces — authAsymIds for protein_get_annotations.chain, labelAsymIds for protein_compare_structures.chain. Present when the call used source experimental (computed-model IDs included); omitted under source predicted or best_available 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.'),
+        .describe('Bound non-polymer components. Present when the call used source experimental; omitted under source predicted or best_available, when the entry binds none, or when the record carries no ligand data.'),
     provider: z.string().optional().describe('Model provider (predicted / best_available).'),
     confidence: z
         .number()
@@ -84,7 +84,7 @@ const structureRecordSchema = z
         pdb: z.string().optional().describe('PDB-format coordinate file URL.'),
         bcif: z.string().optional().describe('Binary CIF coordinate file URL.'),
     })
-        .describe('Coordinate file download URLs.'),
+        .describe('Coordinate file download URLs. A format with no published file is omitted — e.g. pdb for large entries archived as mmCIF only.'),
     coordinateFormat: z
         .enum(['cif', 'pdb', 'bcif'])
         .optional()
@@ -97,7 +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. 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.`,
+    description: `Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs, 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 fetched under source "experimental", computed models included, 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: [
         {
@@ -125,7 +125,7 @@ export const getStructure = tool('protein_get_structure', {
         include_coords: z
             .boolean()
             .default(false)
-            .describe('Inline coordinate-file content (cif). Off by default — URLs are always returned.'),
+            .describe('Inline coordinate-file content — mmCIF, or PDB format when no mmCIF URL is available; coordinateFormat names which. Off by default — URLs are always returned.'),
         sections: z
             .array(z.string())
             .optional()
@@ -166,7 +166,7 @@ export const getStructure = tool('protein_get_structure', {
     enrichment: {
         requested: z
             .number()
-            .describe('Number of IDs in the original request (input.ids.length), before the batch cap was applied.'),
+            .describe('Number of IDs in the original request, 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.'),
@@ -174,7 +174,7 @@ export const getStructure = tool('protein_get_structure', {
         notice: z
             .string()
             .optional()
-            .describe('Every applicable advisory joined into one string: batch cap, partial failures, coordinate-budget overflow, and failed coordinate inlining.'),
+            .describe('Every applicable advisory joined into one string: batch cap, partial failures, a computed model whose provider coordinate lookup failed (only its BinaryCIF URL listed), coordinate-budget overflow, and failed coordinate inlining.'),
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
@@ -193,8 +193,8 @@ export const getStructure = tool('protein_get_structure', {
         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.`, { ...ctx.recoveryFor('mixed_id_types') });
         }
-        const { structures, failed } = input.source === 'experimental'
-            ? await fetchExperimental(ids, ctx)
+        const { structures, failed, notices: resolutionNotices, } = input.source === 'experimental'
+            ? await fetchExperimental(ids, cfg.fanoutConcurrency, ctx)
             : await fetchPredictedOrBest(ids, input.source, cfg.fanoutConcurrency, ctx);
         if (structures.length === 0) {
             throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`, { ...ctx.recoveryFor('all_failed') });
@@ -202,6 +202,8 @@ export const getStructure = tool('protein_get_structure', {
         if (failed.length > 0) {
             notices.push(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
         }
+        if (resolutionNotices)
+            notices.push(...resolutionNotices);
         // Inline coordinates when requested (all, or only the re-called sections).
         const inlineSet = input.sections?.length
             ? new Set(input.sections.map((s) => s.toUpperCase()))
@@ -364,12 +366,13 @@ export const getStructure = tool('protein_get_structure', {
 function pct(fraction) {
     return `${Math.round(fraction * 100)}%`;
 }
-async function fetchExperimental(ids, ctx) {
+async function fetchExperimental(ids, concurrency, ctx) {
     const rcsb = getRcsbService();
     const entries = await rcsb.getEntries(ids, ctx);
     const byId = new Map(entries.map((e) => [e.id.toUpperCase(), e]));
     const structures = [];
     const failed = [];
+    const csms = [];
     for (const id of ids) {
         const meta = byId.get(id.toUpperCase());
         if (!meta) {
@@ -381,7 +384,7 @@ async function fetchExperimental(ids, ctx) {
         // their IDs under the default content_type. Read the provenance rather than
         // stamping every resolved ID experimental — that would both contradict the
         // record and credit an AlphaFold/ModelArchive model to the PDB's CC0.
-        structures.push({
+        const record = {
             id: meta.id,
             source: meta.computedModelProvider ? 'predicted' : 'experimental',
             ...(meta.computedModelProvider ? { provider: meta.computedModelProvider } : {}),
@@ -397,14 +400,62 @@ async function fetchExperimental(ids, ctx) {
             // 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'),
-                bcif: rcsb.coordinateFileUrl(meta.id, 'bcif'),
-            },
-        });
+            coordinateUrls: rcsb.coordinateUrls(meta),
+        };
+        structures.push(record);
+        if (meta.computedModelProvider)
+            csms.push({ meta, record });
     }
-    return { structures, failed };
+    // RCSB publishes only BinaryCIF for a computed model; its provider publishes the
+    // text formats. Each lookup degrades to the RCSB BinaryCIF URL on its own row.
+    const notices = [];
+    await mapWithConcurrency(csms, concurrency, async ({ meta, record }) => {
+        const provider = await providerCoordinateUrls(meta, ctx);
+        if (provider === 'unresolved') {
+            notices.push(`AlphaFold DB coordinate lookup did not resolve for ${meta.id}; only its RCSB BinaryCIF URL is listed — fetch the model by UniProt accession with source "predicted" for mmCIF and PDB files.`);
+            return;
+        }
+        record.coordinateUrls = { ...record.coordinateUrls, ...provider };
+    });
+    return { structures, failed, notices };
+}
+/**
+ * Text-format coordinate URLs from a computed model's own provider, keyed on the
+ * provider entry ID RCSB records. AlphaFold DB file names carry a model version,
+ * so they come from its prediction record — the same URLs `source: "predicted"`
+ * returns. A ModelArchive download is addressed by entry ID alone. `'unresolved'`
+ * marks an AlphaFold model whose lookup failed or found nothing; any other
+ * provider has no known download route and contributes nothing.
+ */
+async function providerCoordinateUrls(meta, ctx) {
+    const entryId = meta.computedModelEntryId;
+    if (meta.computedModelProvider === 'ModelArchive' && entryId) {
+        return {
+            cif: `${getServerConfig().modelArchiveBaseUrl}/api/projects/${encodeURIComponent(entryId)}?type=basic__model_file_name`,
+        };
+    }
+    if (meta.computedModelProvider !== 'AlphaFold DB')
+        return {};
+    if (!entryId)
+        return 'unresolved';
+    const model = await getAlphaFoldService()
+        .getPrediction(entryId, ctx)
+        .catch((err) => {
+        ctx.log.warning('AlphaFold coordinate lookup failed', {
+            id: meta.id,
+            error: err instanceof Error ? err.message : err,
+        });
+        return null;
+    });
+    return model ? alphaFoldCoordinateUrls(model) : 'unresolved';
+}
+/** The coordinate URLs an AlphaFold DB prediction record publishes. */
+function alphaFoldCoordinateUrls(model) {
+    return {
+        ...(model.cifUrl ? { cif: model.cifUrl } : {}),
+        ...(model.pdbUrl ? { pdb: model.pdbUrl } : {}),
+        ...(model.bcifUrl ? { bcif: model.bcifUrl } : {}),
+    };
 }
 /**
  * Per-ID failure reason for an identifier that is not accession-shaped. Kept
@@ -449,11 +500,7 @@ async function fetchPrediction(accession, ctx) {
         ...(typeof model.meanPlddt === 'number' ? { meanPlddt: model.meanPlddt } : {}),
         ...(model.confidenceBuckets ? { confidenceBuckets: model.confidenceBuckets } : {}),
         ...(model.paeDocUrl ? { paeDocUrl: model.paeDocUrl } : {}),
-        coordinateUrls: {
-            ...(model.cifUrl ? { cif: model.cifUrl } : {}),
-            ...(model.pdbUrl ? { pdb: model.pdbUrl } : {}),
-            ...(model.bcifUrl ? { bcif: model.bcifUrl } : {}),
-        },
+        coordinateUrls: alphaFoldCoordinateUrls(model),
     };
 }
 async function fetchBest(accession, ctx) {
@@ -474,12 +521,12 @@ async function fetchBest(accession, ctx) {
     // best-effort — a failed lookup must not drop the structure the agent already has.
     const rcsb = getRcsbService();
     let pdbId;
-    let title;
+    let entry;
     if (isExperimental && best.modelIdentifier) {
         pdbId = best.modelIdentifier.toUpperCase();
-        const entries = await rcsb.getEntries([pdbId], ctx).catch(() => []);
-        title = entries[0]?.title;
+        entry = (await rcsb.getEntries([pdbId], ctx).catch(() => []))[0];
     }
+    const title = entry?.title;
     return {
         id: summary.accession,
         source: isExperimental ? 'experimental' : 'predicted',
@@ -498,12 +545,10 @@ async function fetchBest(accession, ctx) {
             best.confidenceType?.toLowerCase() === 'plddt'
             ? { meanPlddt: best.confidenceAvgLocalScore }
             : {}),
+        // The entry record (when the best-effort lookup succeeded) says whether a
+        // PDB-format file exists; without it the URL set matches an unreported entry.
         coordinateUrls: pdbId
-            ? {
-                cif: rcsb.coordinateFileUrl(pdbId, 'cif'),
-                pdb: rcsb.coordinateFileUrl(pdbId, 'pdb'),
-                bcif: rcsb.coordinateFileUrl(pdbId, 'bcif'),
-            }
+            ? rcsb.coordinateUrls(entry ?? { id: pdbId })
             : best.modelUrl
                 ? coordinateUrlFor(best.modelUrl)
                 : {},
@@ -532,8 +577,11 @@ async function inlineCoordinates(structures, inline, concurrency, ctx) {
             : s.coordinateUrls.pdb
                 ? ['pdb', s.coordinateUrls.pdb]
                 : null;
-        if (!pick)
+        // BinaryCIF is binary, so a record with no text format cannot be inlined.
+        if (!pick) {
+            failures.push(s.id);
             return;
+        }
         try {
             s.coordinates = await fetchText(pick[1], ctx, {
                 operation: 'getStructure.inlineCoordinates',

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

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

	@@ -1 +1 @@
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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;AAmDjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqR3B,CAAC"}

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

@@ -10,7 +10,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { buildFacetSpec, FACET_DIMENSION_NAMES } from '../../../services/rcsb/facets.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
-import { entryIdOf } from '../../../services/shared/identifiers.js';
+import { entryIdOf, isComputedModelId } from '../../../services/shared/identifiers.js';
 import { CONTENT_TYPE_SCOPES, coverageNotices, flatFacetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
 /**
  * Zero-hit advice, per scope. Only the two single-universe scopes have a wider
@@ -22,10 +22,6 @@ const ZERO_HIT_NOTICE = {
     predicted: 'No predicted models matched. Predicted search covers computed models indexed by RCSB; widen content_type to "all" to include experimental structures.',
     all: 'No structures matched in either the experimental or computed-model universe — content_type "all" is already the widest scope. Broaden the query or drop filters.',
 };
-/** A computed-model identifier (AlphaFold / ModelArchive) vs an experimental PDB entry. */
-function isPredictedId(id) {
-    return /^(AF|MA)_/i.test(id);
-}
 /** Pull a UniProt accession out of a computed-model identifier when present (`AF_AFP69905F1` → `P69905`). */
 function accessionFromCsm(id) {
     return /AF_AF([A-Z0-9]+?)F\d+$/i.exec(id)?.[1]?.toUpperCase();
@@ -50,7 +46,7 @@ function truncationNotice(dimensions, cap, sequenceSearch) {
 }
 export const searchStructures = tool('protein_search_structures', {
     title: 'protein-mcp-server: search structures',
-    description: 'Search experimental (PDB) and predicted (computed-model) protein structures by free text, protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, and resolution filters. Returns ranked hits; the experimental page is enriched with title, method, resolution, and organism. Chain hit IDs into protein_get_structure. Optionally returns a facet breakdown (counts by method / organism / release year / …) alongside the hits at no extra call. A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) lists unfiltered alternatives by design — it does not constrain by its own active filter, so you can see sibling values to pivot to. Numeric histogram buckets (resolution, molecular weight) carry explicit rangeFrom/rangeTo bounds so a boundary label is unambiguous.',
+    description: 'Search experimental (PDB) and predicted (computed-model) protein structures by free text, protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, and resolution filters. Returns ranked hits; the experimental page is enriched with title, method, resolution, and organism. Chain hit IDs into protein_get_structure. Optionally returns a facet breakdown (counts by method / organism / release year / …) alongside the hits in the same response. A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) lists unfiltered alternatives by design — it does not constrain by its own active filter, so you can see sibling values to pivot to. Numeric histogram buckets (resolution, molecular weight) carry explicit rangeFrom/rangeTo bounds so a boundary label is unambiguous.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -99,12 +95,12 @@ export const searchStructures = tool('protein_search_structures', {
             .min(0)
             .max(1)
             .optional()
-            .describe('Minimum sequence identity (0–1) for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold would never reach RCSB. Default 0.'),
+            .describe('Minimum sequence identity (0–1) for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold filters only a sequence search. Default 0.'),
         max_evalue: z
             .number()
             .positive()
             .optional()
-            .describe('Maximum E-value for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold would never reach RCSB. Default 1.'),
+            .describe('Maximum E-value for a sequence search. Requires sequence — supplying it without one is rejected, since the threshold filters only a sequence search. Default 1.'),
         content_type: z
             .enum(['experimental', 'predicted', 'all'])
             .default('all')
@@ -129,7 +125,7 @@ export const searchStructures = tool('protein_search_structures', {
             entityId: z
                 .string()
                 .optional()
-                .describe('Matched polymer-entity ID for experimental sequence hits; id remains the chainable PDB entry ID.'),
+                .describe('Matched polymer-entity ID for sequence hits (e.g. 4HHB_1, AF_AFP69905F1_1); id remains the chainable entry ID.'),
             source: z
                 .enum(['experimental', 'predicted'])
                 .describe('Which universe the hit came from.'),
@@ -218,7 +214,7 @@ export const searchStructures = tool('protein_search_structures', {
             start: input.start,
         }, ctx, facetSpecs);
         const experimentalIds = [
-            ...new Set(result.hits.filter((h) => !isPredictedId(h.id)).map((h) => entryIdOf(h.id))),
+            ...new Set(result.hits.filter((h) => !isComputedModelId(h.id)).map((h) => entryIdOf(h.id))),
         ];
         const metaById = new Map();
         if (experimentalIds.length > 0) {
@@ -238,8 +234,12 @@ export const searchStructures = tool('protein_search_structures', {
         // `notice` is a single last-wins field, so the zero-hit advice, the capped-facet
         // advice, and one fragment per under-covered facet dimension compose into ONE string.
         const notices = [];
+        // An empty page with a nonzero total is an offset past the end, not a query
+        // that matched nothing — the two need opposite next moves.
         if (hits.length === 0)
-            notices.push(ZERO_HIT_NOTICE[input.content_type]);
+            notices.push(result.total === 0
+                ? ZERO_HIT_NOTICE[input.content_type]
+                : `start ${input.start} is past the end of the ${result.total} matches. Re-call with a lower start to read a populated page.`);
         if (facets) {
             const capped = facets.filter((f) => f.truncated).map((f) => f.dimension);
             if (capped.length > 0)
@@ -276,20 +276,25 @@ export const searchStructures = tool('protein_search_structures', {
 });
 /** Build one output hit, folding in enrichment metadata when available. */
 function toHit(hit, metaById, sequenceSearch) {
-    if (isPredictedId(hit.id)) {
-        const accession = accessionFromCsm(hit.id);
+    // A sequence search returns polymer entities in both universes (4HHB_1,
+    // AF_AFP69905F1_1); `id` is the chainable entry and `entityId` the matched entity.
+    const entryId = entryIdOf(hit.id);
+    const identity = {
+        id: sequenceSearch ? entryId : hit.id,
+        ...(sequenceSearch ? { entityId: hit.id } : {}),
+    };
+    if (isComputedModelId(hit.id)) {
+        const accession = accessionFromCsm(identity.id);
         return {
-            id: hit.id,
+            ...identity,
             source: 'predicted',
             score: hit.score,
             ...(accession ? { uniprotAccession: accession } : {}),
         };
     }
-    const entryId = entryIdOf(hit.id);
     const meta = metaById.get(entryId);
     return {
-        id: sequenceSearch ? entryId : hit.id,
-        ...(sequenceSearch ? { entityId: hit.id } : {}),
+        ...identity,
         source: 'experimental',
         score: hit.score,
         ...(meta?.title ? { title: meta.title } : {}),