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mahynotch

ChimeraX MCP Server

by mahynotch

set_background

Change the background color of the 3D view to white, black, or a specified hex color for improved contrast and visualization.

Instructions

Set the background color (white, black, hex). Aliases: background, bg color.

Example: set_background("white")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
colorYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

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

No annotations provided, so description carries full burden. It describes the action and valid inputs but does not disclose effects on other aspects (e.g., persistence, interaction with snapshots). Adequate for a simple setter.

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?

Extremely concise: two sentences and an example, front-loaded with purpose. Every element earns its place with no redundancy.

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 single-parameter tool with an output schema, the description covers the core functionality and allowed values. Could mention that it changes the view background, but the purpose is sufficiently clear.

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?

Schema has 0% coverage with no enum or description for the 'color' parameter. Description adds that white, black, and hex values are accepted, plus an example, providing essential meaning beyond the bare schema.

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 verb 'Set' and the resource 'background color', and lists valid values (white, black, hex). This distinguishes it from sibling tools like 'color_structure' which modify molecule colors.

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 vs alternatives like 'color_structure' or other visualization tools. No mention of prerequisites or context.

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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