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protein-blender-mcp

protein-blender-mcp

by OmarArias-Gaguancela
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

delete_molecule

Remove a molecule from the Blender scene to clear unwanted structures before styling or rendering.

Instructions

Remove a molecule from the scene.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "molecule": "<molecule>"
    },
    "name": "delete_molecule"
  }
}

Input Schema

NameRequiredDescriptionDefault
moleculeYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.0

TDQS

C2.7/5.0
Behavior2/5

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

No annotations are provided, so the description carries the full burden. It doesn't disclose whether deletion is permanent or undoable, what happens if the molecule doesn't exist, whether it affects other scene state, or what the response looks like. For a destructive mutation tool this is a significant gap.

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 short, front-loaded sentence with no wasted wording. Brevity is fine here, though it edges toward under-specification rather than tightness.

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 is simple (one required string param, no output schema), but with zero annotations and zero schema descriptions, the definition must explain identifier format and deletion semantics. Neither is covered, so an agent would be guessing on both invocation and consequences.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0% and the description adds nothing about the single parameter — it doesn't say whether "molecule" expects a name, index, ID, or SMILES-like identifier, nor whether it must match an existing scene object. With low coverage, the description should compensate but does not.

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 uses a specific verb ("Remove") plus a specific resource ("molecule") and a scope ("from the scene"). An agent can distinguish it from siblings like fetch_structure or add_style, though it doesn't name any sibling explicitly.

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 prerequisites (e.g., whether the molecule must already be loaded), and no alternatives named among the 12 sibling tools. The purpose is implied only by the verb itself.

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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