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util_cbam

Color atoms in a selected molecule region, setting carbons to magenta for visual distinction in PyMOL.

Instructions

Colors by atom, magenta carbons (Color By Atom, Magenta)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoall

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations provided, so the description must disclose behavioral traits. It only states the coloring action without mentioning side effects, state changes, or requirements like selection scope beyond the default 'all'.

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

Conciseness3/5

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

The description is concise (single sentence) but too brief to be effective. It omits essential details, making it inadequate for a tool with siblings and parameters.

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?

Given the presence of many sibling color utilities and an optional parameter, the description lacks completeness. It does not explain the coloring scheme or selection effect. An output schema exists but does not compensate for the missing contextual information.

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

Parameters1/5

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

The input schema has one parameter 'selection' (default 'all', optional) with no description. The description does not reference the parameter at all, adding no meaning beyond the schema. Schema coverage is 0%, so the description should compensate but fails.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states it 'Colors by atom, magenta carbons', indicating a specific action on atoms (carbons colored magenta). It distinguishes from sibling color utilities like util_cbab (likely blue) by specifying the color, but lacks detail on what 'Color By Atom' means.

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 such as util_cbab or util_color_by_element. The description does not mention context, prerequisites, or exclusions.

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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