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mahynotch

ChimeraX MCP Server

by mahynotch

hide_surface

Hide the displayed molecular surface to reveal underlying structural details.

Instructions

Hide molecular surface. Aliases: remove surface, surface off.

Example: hide_surface("#1")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
specNoall

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations are provided, and the description does not disclose behavioral traits such as scope (e.g., applies to all models by default), reversibility, or side effects. The minimal description adds little beyond the tool name.

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

Conciseness5/5

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

The description is extremely concise: one-line purpose, aliases, and an example. It is front-loaded and wastes no space, though more detail could be added without breaking conciseness.

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?

Given the tool's simplicity (one optional parameter), the description is somewhat adequate but lacks explanation of the 'spec' parameter's semantics and the output schema. It could be more complete with minimal additions.

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%, and the description only shows the parameter in an example without explaining its syntax or meaning. The example helps but does not fully compensate for the lack of parameter documentation.

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 'Hide molecular surface' with aliases and an example, making the verb and resource unambiguous. It is distinct from sibling tools like 'show_surface'.

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 example 'hide_surface("#1")' provides a concrete usage case, but there is no explicit guidance on when to use this tool versus alternatives like 'hide_atoms' or 'show_surface'.

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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