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Glama

color

Idempotent

Applies a named PyMOL hue to a molecular selection; use atomic mode to tint non-carbon atoms by element.

Instructions

Sets the color for a selection.

Input 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

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.5.1
    • addedInput schema / properties / color_name / description
      Added value: +"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."
    • addedInput schema / properties / selection / description
      Added value: +"PyMOL selection string."
  2. First observedv1.2.1

TDQS

C2.9/5.0
Behavior2/5

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

Annotations already declare the mutation profile (readOnlyHint=false, idempotentHint=true, destructiveHint=false), so the agent knows this changes session state reversibly and repeatably. The description adds nothing beyond that: it does not say what gets modified (atom colors within the selection), how the change interacts with rendering, or how to revert it. With annotations present the bar is lower, but a zero-value description earns only a 2.

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?

A single nine-word sentence with no waste and a front-loaded verb, which is appropriate for a simple two-parameter operation. It is arguably over-terse rather than padded, so conciseness is a strength here.

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?

The tool is low complexity (two params, full schema coverage, output schema present), so the description does not need to explain return values. However, for a session-mutating tool it still omits what 'setting a color' affects and how the 'atomic' option differs in behavior, leaving it just minimally adequate.

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%, and the schema itself documents both parameters thoroughly, including the default selection of 'all' and an extensive list of valid color names plus the special 'atomic' value. The description contributes no additional parameter meaning, so the baseline 3 applies.

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 gives a specific verb and resource ('sets the color') plus the target ('for a selection'), so an agent knows exactly what operation is performed. It does not differentiate itself from siblings that also change coloring, such as util_color_by_element, spectrum, util_rainbow, or util_chainbow, leaving the agent to infer that this is the manual, per-selection coloring primitive.

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 like util_color_by_element (element-based coloring) or spectrum (gradient coloring), nor any mention of prerequisites such as having a valid selection loaded. The intended use can only be inferred from the phrase 'for a selection'.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.