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color

Set the shade of a molecular selection in PyMOL. Provide a shade name and optional selection to highlight or differentiate structures.

Instructions

Sets the color for a selection.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoPyMOL selection string.all
color_nameYesA PyMOL color. Common names: ``red``, ``blue``, ``green``, ``yellow``, ``magenta``, ``cyan``, ``orange``, ``salmon``, ``marine``, ``forest``, ``palegreen``, ``skyblue``, ``violet``, ``grey50``, ``white``, ``black``. Use ``atomic`` to color non-carbon atoms by element while leaving carbons untouched.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

With no annotations, the description carries the full burden of behavioral disclosure. It merely says 'Sets the color' which restates the purpose. It does not disclose whether existing colors are overridden, how it interacts with representations, or any side effects.

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?

The description is one sentence with no wasted words. It is concise and front-loaded. However, it is extremely terse and lacks any additional context, which slightly reduces effectiveness despite being well-structured.

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 low complexity and rich schema, the description is still incomplete. It lacks usage guidance, differentiation from siblings, and any behavioral context. The presence of an output schema does not compensate for the missing information about when and how to use this tool.

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?

Schema description coverage is 100% (both 'selection' and 'color_name' have descriptions). The tool description adds no parameter information beyond the schema, so the baseline 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 states a specific verb and resource: 'Sets the color for a selection.' This is clear and unambiguous. However, it does not differentiate from sibling tools like 'spectrum' or 'util_color_by_element' that also deal with coloring.

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 any context, prerequisites, or exclusions. For example, it does not say when to use 'color' instead of 'util_rainbow' or 'spectrum'.

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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