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Assembly

assembly
Read-onlyIdempotent

"Biological assembly of [pdb_id]" / "functional oligomer for [PDB entry]" — fetch a biological assembly record (the functional oligomeric unit, which often differs from the crystallographic asymmetric unit). Use when you need the actual functional form of a protein (dimer / tetramer / etc.) rather than the crystal contents.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes
assembly_idNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. First observed

TDQS

A3.7/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnly, idempotent, and non-destructive hints, so the safety profile is covered. The description adds useful conceptual context about biological assemblies differing from asymmetric units, but doesn't disclose additional behavioral traits like error handling or default assembly selection.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is two sentences long and relatively concise. The first sentence is slightly clunky with quotes, but the second sentence adds clear usage guidance without superfluous detail.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool with 2 parameters and an output schema, the description is adequate but leaves gaps. It explains the core purpose and usage, but does not clarify assembly_id semantics or default behavior when assembly_id is omitted. The output schema likely covers return values, so that is not a major issue.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It implicitly references pdb_id via placeholders like '[pdb_id]' and 'PDB entry', but does not explain the meaning or usage of assembly_id. The description provides only minimal parameter context.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states the tool 'fetch[es] a biological assembly record', clearly specifying the action and resource. It also distinguishes biological assembly from the crystallographic asymmetric unit, setting it apart from sibling tools like 'structure'.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides explicit guidance: 'Use when you need the actual functional form of a protein (dimer / tetramer / etc.) rather than the crystal contents.' This gives clear when-to-use context, though it doesn't explicitly name an alternative tool.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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TDQS

A3.7/5.0
Disambiguation2/5

ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are nearly identical in purpose, and structure/summary both fetch PDB entries. The server name 'Rcsb Pdb' doesn't match most tools, which are Pipeworx data tools, compounding ambiguity.

Naming Consistency3/5

Mostly snake_case verb_noun, but verbs are inconsistent (ask, discover, generate, list, recall) and some names are noun phrases (entity_profile, polymarket_edges). No clear pattern unifies the set.

Tool Count2/5

37 tools is excessive for a server ostensibly about RCSB PDB; only 6 tools relate to PDB while 31 serve unrelated Pipeworx functionality. The count feels like a bundled grab-bag rather than a focused toolset.

Completeness3/5

The PDB-specific tools cover the core operations (search, fetch, assembly, ligand, polymer entity), so the structural biology surface is mostly complete. However, the server's overall purpose is muddled, and the Pipeworx tools are a separate domain that happens to be bundled in, making it unclear what 'completeness' even means for this server.