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N283T

chimerax-mcp-plus

by N283T

chimerax_open

Open molecular structures from local file paths, PDB IDs, or URLs directly in ChimeraX for visualization and analysis.

Instructions

Open a structure file or fetch from PDB.

Args: path_or_id: Local file path, PDB ID (e.g., "1a0s"), or URL

Returns: Result of the open command.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
path_or_idYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

No annotations are provided, so the description must disclose behavioral traits. It only says 'Result of the open command' without detailing potential side effects (e.g., loading into the current session, overwriting existing models, network access for PDB fetch, or error handling). This is insufficient for an agent to fully anticipate the tool's impact.

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 concise and well-structured with a summary, Args, and Returns sections. The Returns line is generic and adds little value, but the overall layout is efficient and front-loaded with the core purpose.

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 one-parameter tool, the input semantics are well covered, and the presence of an output schema means return details are not required. However, without annotations, the description omits behavioral context about session state changes, network dependencies, or failure modes, making it only moderately complete.

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

Parameters5/5

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

The input schema has zero description coverage for the only parameter. The description compensates fully by defining 'path_or_id' as a local file path, a PDB ID (with example '1a0s'), or a URL, giving clear semantics that the schema lacks.

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 clearly states the tool's function: 'Open a structure file or fetch from PDB.' It specifies the resource (structure files, PDB entries) and the verb (open/fetch), and it is distinct from sibling tools like 'chimerax_models' (list models) and 'chimerax_run' (execute commands).

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

Usage Guidelines3/5

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

The description gives basic context about what the tool does (open files or fetch PDB) but does not explicitly state when to use it versus alternatives such as 'chimerax_session_open' or 'chimerax_view'. No exclusions, prerequisites, or preference conditions are mentioned, leaving usage to be implied from the name.

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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