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color

Set the color of molecular selections in PyMOL. Choose from standard color names or use 'atomic' to color non-carbon atoms by element.

Instructions

Sets the color for a selection.

Args: color_name: A 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. selection: PyMOL selection string.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
selectionNoall
color_nameYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior2/5

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

No annotations are provided, so the description carries full burden. However, it only describes the basic action (sets color) without disclosing side effects, persistence, or whether it modifies underlying atom properties. Simple but lacking depth for a mutation tool.

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?

The description is one paragraph with a bullet list of color names, well-organized and concise. Every sentence adds value without redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need not be explained. However, given many sibling tools for coloring (e.g., 'spectrum', 'util_color_by_element'), the description lacks differentiation. It also doesn't note the default selection ('all') explicitly, though schema shows it.

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 coverage is 0%, so description must compensate. For 'color_name', it lists common names and explains 'atomic', adding significant meaning. For 'selection', it only says 'PyMOL selection string' (minimal). Partially compensates.

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 tool's purpose: 'Sets the color for a selection.' It specifies the verb (sets), the resource (color), and the scope (a selection). This is specific and distinct from siblings like 'spectrum' which applies gradients.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides a list of valid color names and explains the special 'atomic' option, but it does not give explicit guidance on when to use this tool versus alternatives like 'spectrum' or 'util_color_by_element'. No when-not-to-use or comparison with 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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