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mahynotch

ChimeraX MCP Server

by mahynotch

clear_labels

Remove all labels from your molecular visualization to declutter the view. This action hides or deletes all annotations.

Instructions

Remove all labels. Aliases: delete labels, hide labels, unlabel.

Example: clear_labels()

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations exist, so the description must disclose behavior. It only states 'Remove all labels' without detailing side effects, undo capability, or what happens to the underlying structure. The behavior is minimally described.

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 very concise, including aliases and an example. It wastes no words but could be structured to include more context. Still, it is efficient and front-loaded.

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

Completeness4/5

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

For a simple tool with no parameters and an existing output schema, the description is fairly complete. It covers the basic action and provides aliases, but lacks details on return values or confirmation of removal.

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

Parameters4/5

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

The tool has no parameters, and the schema coverage is 100% (no params to describe). The description adds no parameter info but is not required to. Baseline for 0 params is 4.

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 action 'Remove all labels' and provides aliases. It is distinct from sibling tools like 'label_residues' which adds labels, making the purpose unambiguous.

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

Usage Guidelines2/5

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

No guidance is provided on when to use this tool versus alternatives. Even though the name implies its use, there is no explicit context about when not to use or how it compares to other label-related tools among siblings.

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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