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util_cbam

Idempotent

Recolors atoms in a PyMOL selection with magenta carbons to visually distinguish molecular regions. Defaults to coloring the entire structure when no selection is provided.

Instructions

Colors by atom, magenta carbons (Color By Atom, Magenta)

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "util_cbam"
  }
}

Input Schema

NameRequiredDescriptionDefault
selectionNoWhat to recolour. Defaults to everything.all

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.5.1
    • addedInput schema / properties / selection / description
      Added value: +"What to recolour. Defaults to everything."
  2. First observedv1.2.1

TDQS

C2.5/5.0
Behavior2/5

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

Annotations declare readOnlyHint=false, idempotentHint=true and destructiveHint=false, so the safety profile is covered. The description adds nothing beyond that: it does not say the change applies to the whole session representation by default, whether prior colors are overwritten, or how it interacts with other color schemes. With annotations present the bar is lower, but the description contributes essentially no behavioral context.

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?

It is short and arguably front-loaded, but the parenthetical '(Color By Atom, Magenta)' merely restates the preceding fragment in expanded form, wasting the only second half of the sentence on redundancy rather than on disambiguation from siblings.

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?

An output schema exists, so return values need not be explained, but for a tool embedded in a large family of near-identical color variants the description should at minimum clarify its role relative to those siblings. As written, an agent has almost nothing to disambiguate 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 single 'selection' parameter already documents 'What to recolour. Defaults to everything.' The description never references the selection parameter, so it adds no meaning beyond the schema; the baseline 3 applies.

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 identifies a coloring operation with magenta carbons, which hints at a specific color-by-atom scheme. However, 'Colors by atom, magenta carbons' is awkwardly phrased and does not distinguish it from the many near-identical siblings (util_cbay, util_cbas, util_cbab, util_cbao, util_cbap, util_cbak), so an agent still cannot tell which variant to pick from the text alone.

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 when-to-use guidance, no mention of the alternative color-by-atom variants, and no note about when magenta carbons are preferable. The agent is left to infer that this is one of a family of mutually exclusive coloring schemes.

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