Retrieve MOLE tunnel annotations for a PDB entry using its PDB ID, optionally specifying an assembly ID; defaults to the PDBe-preferred assembly.
Returns MOLE tunnel annotations for a PDB entry. When assembly_id is omitted, the PDBe-preferred assembly is used.
| Name | Required | Description | Default |
|---|---|---|---|
| pdb_id | Yes | 4-character PDB id code. title: Pdb Id description: 4-character PDB id code. | |
| assembly_id | No | Numerical assembly id code |
Changes observed during successful MCP inspections.
v2.0.1Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered. The description usefully adds that omitting assembly_id falls back to the PDBe-preferred assembly, but it says nothing about return shape, whether tunnels can be empty for an entry, or why idempotentHint is false.
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?
Two sentences, zero filler, with the core purpose front-loaded and the optional-parameter default immediately after. Nothing is redundant with the title or restates the name.
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?
For a simple two-parameter read tool with no output schema and full schema coverage, the description covers purpose and the one non-obvious parameter behavior. A brief note on what a tunnel annotation contains, or the empty-result case, would make it fully self-sufficient.
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 coverage is 100%, so both parameters are documented structurally, and the description goes beyond the schema by explaining the fallback semantics of the optional assembly_id (PDBe-preferred assembly). That is genuine added meaning, though the format of pdb_id is left to the schema.
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?
"Returns MOLE tunnel annotations for a PDB entry" gives a specific verb (returns) and a specific resource (MOLE tunnel annotations) scoped to a PDB entry. It is clearly distinct from sibling tools such as bind_sites or ligand interactions, though the distinction is inferred from the subject matter rather than stated.
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?
The description implies use when tunnel/pocket annotations for a structure are wanted and states the default-assembly behavior, but it never explicitly says when to use this versus related PDBe annotation endpoints or what prerequisites (e.g. a MOLE-annotated entry) apply.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.