Skip to main content
Glama

spectrum

Apply a color spectrum to a molecular selection based on properties like B-factor, occupancy, residue index, or partial charge.

Instructions

Colors selection in a spectrum

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
paletteNoColour ramp, e.g. ``rainbow``, ``blue_white_red``, ``cyan_white_magenta``, ``green_yellow_red``.rainbow
selectionNoPyMOL selection string, e.g. "1abc and chain A". See the module note for syntax.all
expressionYesAtom property to colour by: ``b`` (B-factor or pLDDT), ``q`` (occupancy), ``count``, ``resi``, ``pc`` (partial charge).

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 must disclose behavioral details, but it only states the basic coloring action. It does not mention that colors are assigned to atoms based on a property, that prior color assignments may be overwritten, or any other 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 a single short sentence with no filler or redundant information. It front-loads the core action, though it is grammatically awkward 'in a spectrum' and could be phrased more clearly.

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 description, combined with the fully documented parameters and existence of an output schema, gives the agent a minimal but usable picture of a spectrum-coloring command. Missing details are the absence of usage context and side-effect disclosure, but the schema covers the parameter semantics.

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?

All three parameters have descriptive schema text (palette, selection, expression), so the description adds no additional parameter meaning. The schema already explains the palette options, selection syntax, and property to color by, earning a baseline score of 3.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description 'Colors selection in a spectrum' names a verb and object, indicating the tool colors a selection using a spectrum. However, it does not specify that coloring is driven by an atom property (e.g., B-factor, occupancy) or explain how it differs from sibling commands like 'color' or 'util_rainbow'.

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?

No guidance is given about when to use this tool versus alternative coloring/spectrum tools. It does not mention prerequisites, exclusions, or fallback tools, leaving the agent to infer appropriate usage from the name and schema.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/chemrich/MCPymol'

If you have feedback or need assistance with the MCP directory API, please join our Discord server