@cyanheads/protein-mcp-server 0.4.0 → 0.4.1

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

@@ -1,11 +1,24 @@
 /**
- * @fileoverview Shared Zod output schemas and helpers for the facet breakdown
- * surfaced by `protein_analyze_collection` and `protein_search_structures`. Nesting
- * is bounded to two levels (a dimension's buckets may each carry one child
- * dimension), matching the deepest cross-tab the facet engine produces.
+ * @fileoverview Shared schemas and helpers for the two tools that expose a facet
+ * breakdown and a `content_type` scope — `protein_analyze_collection` and
+ * `protein_search_structures`. Facet nesting is bounded to two levels (a
+ * dimension's buckets may each carry one child dimension), matching the deepest
+ * cross-tab the facet engine produces. Every dimension position also reports its
+ * coverage gap, so buckets that sum to less than the stated total say so.
  * @module mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * The agent-facing `content_type` scope → the RCSB content universes it selects.
+ * `all` names both members explicitly: omitting `results_content_type` upstream
+ * is experimental-only, not a union. Shared so the two tools that expose the
+ * enum cannot drift apart on what a scope means.
+ */
+export const CONTENT_TYPE_SCOPES = {
+    experimental: ['experimental'],
+    predicted: ['computational'],
+    all: ['experimental', 'computational'],
+};
 /** A flat (leaf) facet bucket. */
 const leafBucketSchema = z
     .object({
@@ -30,6 +43,9 @@ const childDimensionSchema = z
         .boolean()
         .optional()
         .describe('True when this nested bucket list was capped by the per-dimension bucket limit.'),
+    missingValueCount: z
+        .number()
+        .describe('Matches inside the parent bucket that carry no value for this nested attribute, so they fall in no nested bucket. 0 when the nested buckets account for the whole parent bucket.'),
 })
     .describe('A nested cross-tab dimension within a parent bucket.');
 /** A top-level facet bucket, optionally carrying a nested cross-tab dimension. */
@@ -62,6 +78,9 @@ export const facetDimensionSchema = z
         .boolean()
         .optional()
         .describe('True when buckets were capped by the per-dimension bucket limit.'),
+    missingValueCount: z
+        .number()
+        .describe('Matches in scope that carry no value for this attribute, so they count toward the response total but fall in no bucket (e.g. computed models have no experimental method; solution-NMR entries have no diffraction resolution). Independent of truncation — measured before the bucket cap is applied. 0 means no shortfall was detectable: a multi-valued attribute such as organism can place one match in several buckets, which offsets the shortfall rather than adding to it.'),
 })
     .describe('A facet dimension and its aggregation buckets.');
 /** Copy the numeric-histogram range onto an output bucket when present. */
@@ -70,8 +89,32 @@ function withRange(b) {
         ? { rangeFrom: b.rangeFrom, rangeTo: b.rangeTo }
         : {};
 }
-/** Project a domain {@link FacetDimension} to the output shape, capping buckets. */
-export function toFacetOutput(facet, cap) {
+/**
+ * How many of `total` the buckets leave unaccounted for — matches carrying no
+ * value for the faceted attribute, which land in no bucket.
+ *
+ * Two properties carry the correctness:
+ *
+ * - `buckets` must be the UNCAPPED list. Measured after {@link toFacetOutput}
+ *   slices to the bucket cap, the difference would fold in what the cap removed
+ *   — a separate condition the response already discloses through `truncated` /
+ *   `shown` / `cap`.
+ * - The result floors at 0. A multi-valued attribute puts one match in several
+ *   buckets (an entry with two source organisms lands in both), so the sum can
+ *   legitimately exceed the total. That is over-counting, a different phenomenon
+ *   from missing coverage, and this field does not claim to describe it. On a
+ *   dimension that is both multi-valued and sparse the two net out, so 0 means
+ *   "no shortfall detectable", not proof that every match reached a bucket.
+ */
+function missingValueCount(buckets, total) {
+    return Math.max(0, total - buckets.reduce((sum, b) => sum + b.count, 0));
+}
+/**
+ * Project a domain {@link FacetDimension} to the output shape, capping buckets.
+ * `total` is the population the buckets describe — the response total for a
+ * top-level dimension, and the parent bucket's count for a nested one.
+ */
+export function toFacetOutput(facet, cap, total) {
     const truncated = facet.buckets.length > cap;
     return {
         dimension: facet.dimension,
@@ -87,11 +130,13 @@ export function toFacetOutput(facet, cap) {
                             .slice(0, cap)
                             .map((cb) => ({ label: cb.label, count: cb.count, ...withRange(cb) })),
                         ...(c.buckets.length > cap ? { truncated: true } : {}),
+                        missingValueCount: missingValueCount(c.buckets, b.count),
                     })),
                 }
                 : {}),
         })),
         ...(truncated ? { truncated: true } : {}),
+        missingValueCount: missingValueCount(facet.buckets, total),
     };
 }
 /**
@@ -103,21 +148,116 @@ function renderBucket(b) {
     const range = b.rangeFrom !== undefined && b.rangeTo !== undefined ? ` [${b.rangeFrom}–${b.rangeTo})` : '';
     return `${b.label}${range}: ${b.count}`;
 }
+/**
+ * Stands in for a dimension that aggregated to nothing. A bare `**dimension**`
+ * heading with no buckets under it reads as a broken response; say the scope
+ * produced no data instead. Why it is empty (a zero-hit query, or an attribute
+ * the scoped content universe does not carry) is the caller's notice to give.
+ */
+const EMPTY_DIMENSION_LINE = '_No data for this dimension in the current scope._';
+/** Inline twin of {@link EMPTY_DIMENSION_LINE} for a nested cross-tab child that aggregated to nothing. */
+const EMPTY_CHILD_DIMENSION_TEXT = '_no data in this scope_';
+/**
+ * The parenthetical after a dimension's name: the bucket-cap marker and the
+ * coverage gap, in one group so a dimension carrying both does not sprout two
+ * sets of parentheses.
+ */
+function dimensionFlags(d) {
+    const flags = [
+        d.truncated ? 'truncated' : '',
+        d.missingValueCount > 0 ? `${d.missingValueCount} with no value` : '',
+    ].filter(Boolean);
+    return flags.length > 0 ? ` (${flags.join('; ')})` : '';
+}
 /** Render a list of facet dimensions to markdown lines for `format()` parity. */
 export function renderFacets(facets) {
     const lines = [];
     for (const f of facets) {
-        lines.push(`\n**${f.dimension}**${f.truncated ? ' (truncated)' : ''}`);
+        lines.push(`\n**${f.dimension}**${dimensionFlags(f)}`);
+        if (f.buckets.length === 0) {
+            lines.push(EMPTY_DIMENSION_LINE);
+            continue;
+        }
         for (const b of f.buckets) {
             lines.push(`- ${renderBucket(b)}`);
             for (const c of b.children ?? []) {
-                const inner = c.buckets.map(renderBucket).join(', ');
-                lines.push(`  - ${c.dimension} → ${inner}${c.truncated ? ' (truncated)' : ''}`);
+                const inner = c.buckets.length === 0
+                    ? EMPTY_CHILD_DIMENSION_TEXT
+                    : c.buckets.map(renderBucket).join(', ');
+                lines.push(`  - ${c.dimension} → ${inner}${dimensionFlags(c)}`);
             }
         }
     }
     return lines;
 }
+/**
+ * Share of a dimension's scope that must carry no value before the coverage gap
+ * earns prose on top of the always-present `missingValueCount` field.
+ *
+ * 1% separates the two regimes seen in the live data. Below it the difference is
+ * rounding-scale against the distribution the buckets describe — `method` under
+ * `content_type: "experimental"` misses 0.09% — and prose on every response
+ * would be noise. At or above it the buckets describe a visibly different
+ * population than the stated total: `resolution` under `"experimental"` misses
+ * 3.8% to entries with no diffraction resolution, and every experimental-only
+ * dimension misses ~45% of a mixed `"all"` scope.
+ */
+const MATERIAL_COVERAGE_GAP = 0.01;
+/**
+ * Flatten a facet tree to one entry per dimension position. A child dimension
+ * repeats under every parent bucket, so its counts are summed into a single
+ * position — otherwise a 50-bucket cross-tab would yield fifty advisories about
+ * the same attribute. Parent buckets the cap removed are not represented, which
+ * is correct: the aggregate then describes exactly the buckets the response shows.
+ */
+function coveragePositions(facets, total) {
+    const positions = [];
+    for (const f of facets) {
+        positions.push({
+            dimension: f.dimension,
+            missing: f.missingValueCount,
+            scope: total,
+            bucketCount: f.buckets.length,
+        });
+        const children = new Map();
+        for (const b of f.buckets) {
+            for (const c of b.children ?? []) {
+                const acc = children.get(c.dimension) ?? { missing: 0, scope: 0, bucketCount: 0 };
+                acc.missing += c.missingValueCount;
+                acc.scope += b.count;
+                acc.bucketCount += c.buckets.length;
+                children.set(c.dimension, acc);
+            }
+        }
+        for (const [dimension, acc] of children)
+            positions.push({ dimension, ...acc });
+    }
+    return positions;
+}
+/**
+ * Advisory fragments for the dimensions whose coverage gap is material, ready to
+ * join into the shared `notice` field alongside a caller's other advisories.
+ *
+ * A dimension that aggregated to nothing at all is skipped: the empty-dimension
+ * line in `format()` (and, where it applies, the caller's scope notice) already
+ * report it, and quantifying a 100% gap on top adds nothing.
+ */
+export function coverageNotices(facets, total) {
+    const seen = new Set();
+    const notices = [];
+    for (const p of coveragePositions(facets, total)) {
+        if (p.scope <= 0 || p.bucketCount === 0)
+            continue;
+        if (p.missing / p.scope < MATERIAL_COVERAGE_GAP)
+            continue;
+        if (seen.has(p.dimension))
+            continue;
+        seen.add(p.dimension);
+        const pct = ((p.missing / p.scope) * 100).toFixed(1);
+        notices.push(`${p.dimension} buckets cover ${p.scope - p.missing} of ${p.scope} matches; the other ${p.missing} (${pct}%) carry no ${p.dimension} value and fall in no bucket.`);
+    }
+    return notices;
+}
 /** License + citation for one upstream data source that contributed to a response. */
 export const attributionSchema = z
     .object({

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

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package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts

@@ -11,25 +11,25 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     group_by: z.ZodArray<z.ZodEnum<{
         method: "method";
-        organism: "organism";
-        resolution: "resolution";
         molecular_weight: "molecular_weight";
+        organism: "organism";
         polymer_type: "polymer_type";
         release_year: "release_year";
+        resolution: "resolution";
     }>>;
     query: z.ZodOptional<z.ZodString>;
     organism: z.ZodOptional<z.ZodString>;
     method: z.ZodOptional<z.ZodString>;
     max_resolution: z.ZodOptional<z.ZodCoercedNumber<unknown>>;
     content_type: z.ZodDefault<z.ZodEnum<{
+        all: "all";
         experimental: "experimental";
         predicted: "predicted";
-        all: "all";
     }>>;
     interval: z.ZodOptional<z.ZodUnion<readonly [z.ZodCoercedNumber<unknown>, z.ZodEnum<{
-        year: "year";
         month: "month";
         quarter: "quarter";
+        year: "year";
     }>]>>;
     bucket_limit: z.ZodOptional<z.ZodCoercedNumber<unknown>>;
 }, z.core.$strip>, z.ZodObject<{
@@ -50,9 +50,11 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
                     rangeTo: z.ZodOptional<z.ZodNumber>;
                 }, z.core.$strip>>;
                 truncated: z.ZodOptional<z.ZodBoolean>;
+                missingValueCount: z.ZodNumber;
             }, z.core.$strip>>>;
         }, z.core.$strip>>;
         truncated: z.ZodOptional<z.ZodBoolean>;
+        missingValueCount: z.ZodNumber;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_dimension";
@@ -62,5 +64,8 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
 }], {
     readonly scope: z.ZodOptional<z.ZodString>;
     readonly notice: z.ZodOptional<z.ZodString>;
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
 }>;
 //# sourceMappingURL=analyze-collection.tool.d.ts.map

package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4H5B,CAAC"}
+{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwBjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuJ5B,CAAC"}

package/dist/mcp-server/tools/definitions/analyze-collection.tool.js

@@ -9,9 +9,16 @@
 import { tool, z } from '@cyanheads/mcp-ts-core';
 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 { buildFacetSpec, FACET_DIMENSION_NAMES, } from '../../../services/rcsb/facets.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
-import { facetDimensionSchema, renderFacets, toFacetOutput } from './_schemas.js';
+import { CONTENT_TYPE_SCOPES, coverageNotices, facetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
+/**
+ * Dimensions RCSB cannot aggregate over computed models: an AlphaFold /
+ * ModelArchive record carries no experimental method or resolution, so the
+ * facet key is absent from the response rather than returning empty buckets.
+ * The other four dimensions aggregate normally under predicted content.
+ */
+const EXPERIMENTAL_ONLY_DIMENSIONS = new Set(['method', 'resolution']);
 export const analyzeCollection = tool('protein_analyze_collection', {
     title: 'protein-mcp-server: analyze collection',
     description: 'Profile the PDB into distributions and trends over an optional scoping query: counts by method, ' +
@@ -48,7 +55,8 @@ export const analyzeCollection = tool('protein_analyze_collection', {
         content_type: z
             .enum(['experimental', 'predicted', 'all'])
             .default('experimental')
-            .describe('Which structure universe to profile. Default experimental.'),
+            .describe('Which structure universe to profile. Default experimental. Computed models carry no ' +
+            'experimental metadata, so method and resolution return nothing under "predicted".'),
         interval: z
             .union([
             // Coerce the numeric arm: many clients stringify tool args, and "0.5" must
@@ -76,17 +84,21 @@ export const analyzeCollection = tool('protein_analyze_collection', {
     }),
     enrichment: {
         scope: z.string().optional().describe('Echoed scope description for follow-up calls.'),
-        notice: z.string().optional().describe('Advisory note (e.g. bucket truncation, empty scope).'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Advisory note (bucket truncation, empty scope, dimensions with no data under the requested content_type, dimensions whose buckets cover materially less than the total). Carries every applicable advisory in one string.'),
+        truncated: z
+            .boolean()
+            .optional()
+            .describe('True when a dimension had more buckets than the applied cap.'),
+        shown: z.number().optional().describe('Buckets returned for the capped dimension.'),
+        cap: z.number().optional().describe('Per-dimension bucket cap that was applied.'),
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
         const rcsb = getRcsbService();
         const cap = input.bucket_limit ?? cfg.facetBucketCap;
-        const contentType = input.content_type === 'all'
-            ? undefined
-            : input.content_type === 'predicted'
-                ? 'computational'
-                : 'experimental';
         const [primary, secondary] = input.group_by;
         if (!primary)
             throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.', {
@@ -100,12 +112,29 @@ export const analyzeCollection = tool('protein_analyze_collection', {
             ...(typeof input.max_resolution === 'number'
                 ? { maxResolution: input.max_resolution }
                 : {}),
-            ...(contentType ? { contentType } : {}),
+            contentType: CONTENT_TYPE_SCOPES[input.content_type],
         }, [spec], ctx);
-        const out = facets.map((f) => toFacetOutput(f, cap));
-        if (out.some((f) => f.truncated)) {
-            ctx.enrich.notice(`One or more dimensions exceeded ${cap} buckets and were capped; scope the query tighter for the long tail.`);
+        const out = facets.map((f) => toFacetOutput(f, cap, total));
+        // Every advisory writes the same `notice` field (ctx.enrich.truncated routes
+        // through it and is last-wins), and a cross-tab under predicted content can
+        // trip several at once — collect the fragments and emit them as ONE notice.
+        const notices = [];
+        const capped = out.find((f) => f.truncated);
+        if (capped) {
+            ctx.enrich({ truncated: true, shown: capped.buckets.length, cap });
+            notices.push(`One or more dimensions exceeded ${cap} buckets and were capped; scope the query tighter for the long tail.`);
+        }
+        if (input.content_type === 'predicted') {
+            // Deduped: group_by permits the same dimension twice, and "method and
+            // method" would read as two findings.
+            const blind = [...new Set(input.group_by.filter((d) => EXPERIMENTAL_ONLY_DIMENSIONS.has(d)))];
+            if (blind.length > 0) {
+                notices.push(`${blind.join(' and ')} ${blind.length > 1 ? 'are' : 'is'} empty under content_type "predicted": computed models carry no experimental method or resolution metadata. Use content_type "experimental" or "all", or group by organism, polymer_type, release_year, or molecular_weight.`);
+            }
         }
+        notices.push(...coverageNotices(out, total));
+        if (notices.length > 0)
+            ctx.enrich.notice(notices.join(' '));
         const scopeBits = [input.query, input.organism, input.method].filter(Boolean);
         if (scopeBits.length > 0)
             ctx.enrich({ scope: scopeBits.join(' · ') });

package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map

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

@@ -13,13 +13,13 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
         chain: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     reference: z.ZodDefault<z.ZodEnum<{
-        first: "first";
         all_pairs: "all_pairs";
+        first: "first";
     }>>;
     method: z.ZodDefault<z.ZodEnum<{
-        "tm-align": "tm-align";
-        "fatcat-rigid": "fatcat-rigid";
         "fatcat-flexible": "fatcat-flexible";
+        "fatcat-rigid": "fatcat-rigid";
+        "tm-align": "tm-align";
     }>>;
     timeout_s: z.ZodOptional<z.ZodNumber>;
     resume: z.ZodOptional<z.ZodArray<z.ZodObject<{
@@ -30,8 +30,8 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
 }, z.core.$strip>, z.ZodObject<{
     method: z.ZodString;
     reference: z.ZodEnum<{
-        first: "first";
         all_pairs: "all_pairs";
+        first: "first";
     }>;
     pairs: z.ZodArray<z.ZodObject<{
         a: z.ZodString;

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

@@ -14,8 +14,8 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
     chain: z.ZodOptional<z.ZodString>;
     include: z.ZodDefault<z.ZodEnum<{
         all: "all";
-        features: "features";
         domains: "domains";
+        features: "features";
         variants: "variants";
     }>>;
     limit: z.ZodDefault<z.ZodNumber>;

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

@@ -12,9 +12,9 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     ids: z.ZodArray<z.ZodString>;
     source: z.ZodDefault<z.ZodEnum<{
+        best_available: "best_available";
         experimental: "experimental";
         predicted: "predicted";
-        best_available: "best_available";
     }>>;
     include_coords: z.ZodDefault<z.ZodBoolean>;
     sections: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -47,9 +47,9 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
             bcif: z.ZodOptional<z.ZodString>;
         }, z.core.$strip>;
         coordinateFormat: z.ZodOptional<z.ZodEnum<{
+            bcif: "bcif";
             cif: "cif";
             pdb: "pdb";
-            bcif: "bcif";
         }>>;
         coordinates: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;

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

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

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

@@ -79,7 +79,9 @@ const structureRecordSchema = z
 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); "predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); ' +
+        '(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 ' +
@@ -105,7 +107,7 @@ export const getStructure = tool('protein_get_structure', {
         ids: z
             .array(z.string().min(1))
             .min(1)
-            .describe('PDB entry IDs (source experimental) or UniProt accessions (predicted / best_available).'),
+            .describe('PDB entry IDs or computed-model IDs such as AF_AFP69905F1 (source experimental), or UniProt accessions (predicted / best_available).'),
         source: z
             .enum(['experimental', 'predicted', 'best_available'])
             .default('experimental')
@@ -133,7 +135,7 @@ export const getStructure = tool('protein_get_structure', {
             .describe('IDs that could not be resolved (partial success).'),
         attribution: z
             .array(attributionSchema)
-            .describe('Upstream data-source licenses and citations for every source present in structures[] — RCSB PDB for experimental records, AlphaFold DB for predicted. Always present — the attribution obligation travels with the data.'),
+            .describe('Upstream data-source licenses and citations for every source present in structures[] — RCSB PDB for experimental records, the modelling provider (AlphaFold DB, ModelArchive, SWISS-MODEL, …) for predicted ones. Always present — the attribution obligation travels with the data.'),
         overflow: z
             .object({
             sections: z
@@ -301,9 +303,15 @@ async function fetchExperimental(ids, ctx) {
             failed.push({ id, reason: 'No PDB entry found for this ID.' });
             continue;
         }
+        // RCSB serves computed structure models (AF_* / MA_*) from the same entry
+        // endpoint as experimental entries, and protein_search_structures surfaces
+        // 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({
             id: meta.id,
-            source: 'experimental',
+            source: meta.computedModelProvider ? 'predicted' : 'experimental',
+            ...(meta.computedModelProvider ? { provider: meta.computedModelProvider } : {}),
             ...(meta.title ? { title: meta.title } : {}),
             ...(meta.methods && meta.methods.length > 0 ? { method: meta.methods.join(', ') } : {}),
             ...(typeof meta.resolution === 'number' ? { resolution: meta.resolution } : {}),

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