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MCPymol

MCPymol

by chemrich
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
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spectrum

Idempotent

Map atom properties such as B-factor, occupancy, residue index, count, or partial charge to a color ramp across a PyMOL selection for visual structure analysis.

Instructions

Colors selection in a spectrum

Input 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

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed3 schema fields changedv1.5.1
    • addedInput schema / properties / expression / description
      Added value: +"Atom property to colour by: ``b`` (B-factor or pLDDT), ``q`` (occupancy), ``count``, ``resi``, ``pc`` (partial charge)."
    • addedInput schema / properties / palette / description
      Added value: +"Colour ramp, e.g. ``rainbow``, ``blue_white_red``, ``cyan_white_magenta``, ``green_yellow_red``."
    • addedInput schema / properties / selection / description
      Added value: +"PyMOL selection string, e.g. \"1abc and chain A\". See the module note for syntax."
  2. First observedv1.2.1

TDQS

C2.3/5.0
Behavior2/5

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

Annotations already declare the safety profile (idempotent, non-destructive, not read-only, closed-world), so the description is not carrying that burden. However, it adds nothing about what state is changed, that this is a display/coloring operation, or how it interacts with existing color settings, leaving behavior opaque beyond the annotations.

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 a single short phrase with no wasted words, but its brevity comes at the cost of under-specification rather than efficient communication. It is not front-loaded with the key action or resource.

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?

The tool takes three parameters with full schema coverage and has an output schema, so some completeness burden is lifted. Still, for a coloring operation with many closely related siblings, the description fails to establish what makes this tool distinct or when an agent should reach for 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 description coverage is 100%, and the schema already explains palette, selection, and expression with concrete examples. The description adds no parameter meaning beyond the schema, so the baseline 3 applies.

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

Purpose2/5

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

The phrase 'Colors selection in a spectrum' only loosely restates the tool name. It does not specify that the tool applies a color ramp mapped to an atom property over a PyMOL selection, nor does it distinguish this from siblings like color, util_rainbow, or util_chainbow.

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 explicit when-to-use guidance and no mention of when not to use it or which sibling to choose instead. The coloring intent is implied only by the word 'Colors,' leaving the agent to infer the use case from the schema.

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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