polymer_entity"Chain [N] of PDB [ID]" / "sequence of chain in [pdb_id]" — fetch the polymer-entity (protein/DNA/RNA chain) metadata for a specific PDB entry. Returns sequence, source organism, UniProt cross-references, GO annotations. Use to drill into one chain of a multi-chain structure.
| Name | Required | Description | Default |
|---|---|---|---|
| pdb_id | Yes | ||
| entity_id | Yes |
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Changes observed during successful MCP inspections. Dates show when Glama detected each change.
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare read-only, idempotent, open-world, and non-destructive behavior. The description adds value by specifying the exact return content (sequence, source organism, UniProt cross-references, GO annotations), which goes beyond the annotations. It does not cover error cases or rate limits, but these are not critical for a simple fetch.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise and well-structured: it starts with intuitive example queries, then states the action and return fields, and ends with a usage tip. Every sentence earns its place, with no redundancy.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's simplicity (2 plain string params) and the presence of an output schema, the description is complete: it explains what the tool does, what it returns, and when to use it. It lacks only edge-case details, which are not essential for a metadata fetch tool.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema has zero parameter descriptions (0% coverage), but the description's example query formats ('Chain [N] of PDB [ID]' and 'sequence of chain in [pdb_id]') effectively map pdb_id to the PDB entry and entity_id to a chain number. This compensates for the missing schema info, though it leaves some format details implicit.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Description clearly states it fetches polymer-entity metadata for a specific PDB entry, with a specific verb ('fetch'), resource ('polymer-entity (protein/DNA/RNA chain) metadata'), and scope. It distinguishes from siblings like 'assembly' and 'ligand' by emphasizing drill-down into one chain.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Provides explicit usage advice: 'Use to drill into one chain of a multi-chain structure.' However, it does not mention when not to use it or name alternative tools, so it lacks full exclusionary guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Add one secure layer between your agents and this server.
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.
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.
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.
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.