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mahynotch

ChimeraX MCP Server

by mahynotch

label_residues

Add text labels to protein residues, displaying residue name and number by default or custom text for specified residues.

Instructions

Add text labels to residues. Default shows residue name + number. Aliases: annotate, tag residues, show labels.

Example: label_residues("/A:501")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
specYes
labelNodefault

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations provided, and description does not disclose whether labels are appended, replaced, or cleared. Effects on existing labels are unclear, important for a labeling tool.

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?

Concise with minimal fluff. Includes aliases and example. Could be slightly more structured, but front-loads the primary action effectively.

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

Completeness2/5

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

Missing details on whether multiple residues can be labeled at once, how existing labels are handled, or any output expectations. Despite an output schema, the behavioral gaps reduce completeness.

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 coverage is 0%, so description must compensate. It explains spec via example and implies label customizes text, but does not specify format for spec or valid values for label. The default label value 'default' is ambiguous.

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?

Description clearly states 'Add text labels to residues' with default behavior, includes aliases, and provides an example. It distinguishes from sibling 'clear_labels' by focusing on addition vs removal.

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 on when to use this tool versus alternatives. Example shows basic usage but no context for when labeling is appropriate or when to choose other tools.

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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