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util_cbc

Color molecular structures by chain to visually distinguish protein chains. Use with PyMOL selections to highlight different chains for analysis.

Instructions

Colors by chain (Color By Chain)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoWhat to recolour. Defaults to everything.all

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It only states the action (colors by chain) without explaining the color scheme, reversibility, whether it affects all objects or only the selection, or any side effects. This is minimal and insufficient for full transparency.

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 very short but contains redundancy: 'Colors by chain (Color By Chain)' repeats the same information in parentheses. It could be more concise, but it is not overly verbose. A cleaner structure would state the function once without the parenthetical restatement.

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?

The description is insufficient for a tool that modifies visual state. It does not explain the color mapping, whether existing colors are overwritten, or how the selection parameter interacts with the coloring. Despite an output schema being present, the description fails to provide enough context for an agent to know the tool's full impact.

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

Parameters3/5

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

The input schema provides a description for the only parameter 'selection' ('What to recolour. Defaults to everything.'), achieving 100% schema coverage. The tool description adds no parameter information, so the baseline score of 3 is appropriate.

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 'Colors by chain' clearly indicates the tool's function: recoloring structures by chain. It uses a specific verb (Colors) and resource (chain), but it does not distinguish itself from sibling color-related tools such as 'util_chainbow' or 'spectrum'.

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?

There is no guidance on when to use this tool versus alternatives. The description does not mention exclusions, prerequisites, or scenarios where other coloring tools would be more appropriate. This is a clear gap for a tool with many 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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