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util_cbag

Color atoms by atom type with green carbons to highlight protein or ligand structures. Apply to a specific selection or entire molecule.

Instructions

Colors by atom, green carbons (Color By Atom, Green)

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 color scheme (green carbons) but does not reveal whether existing colors are overwritten, how selection affects the outcome, or what happens to other atom types. This is especially problematic for a mutating operation.

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 extremely short and front-loaded, but the parenthetical '(Color By Atom, Green)' redundantly repeats the meaning of 'Colors by atom, green carbons'. This redundancy is unnecessary, though the overall length is appropriate for a simple utility.

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 tool's low complexity and the presence of an output schema and 100% schema description coverage, the description could be sufficient, but it omits critical usage context and behavioral details. The agent cannot confidently decide when to call this tool over its many siblings, and the lack of annotation makes the side effects unclear.

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 schema description coverage is 100%, with the 'selection' parameter described as 'What to recolour. Defaults to everything.' The tool description adds no additional parameter semantics, so the baseline score of 3 applies because the schema already does the heavy lifting.

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 a specific action ('Colors by atom') and a distinguishing detail ('green carbons'), which separates it from sibling color utilities like util_cbc or util_chainbow. The parenthetical '(Color By Atom, Green)' reinforces the intent, though it doesn't explicitly mention how non-carbon atoms are colored.

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 the many sibling color/utility tools, nor any exclusions or alternatives. The description reads as a label rather than usage instructions, leaving the agent to infer applicability from the tool name.

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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