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vmd-hydrate-mcp

vmd-hydrate-mcp

by wjgoarxiv
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

add_representation

Layer multiple molecular representations on the same molecule without clearing previous ones, enabling combined visual styles.

Instructions

Add a representation WITHOUT clearing existing ones — layer several reps (e.g. water as Points + solute as VDW). color is a coloring METHOD (Name, ResName, ResType, Chain, Beta, ...); style is VDW/Lines/Points/ NewCartoon/Licorice/etc.

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": {
      "molid": "<molid>"
    },
    "name": "add_representation"
  }
}

Input Schema

NameRequiredDescriptionDefault
colorNoName
molidYes
styleNoVDW
materialNoOpaque
selectionNoall

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

A3.8/5.0
Behavior3/5

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

No annotations provided. The description discloses that it adds without clearing and explains the color and style fields. However, it does not mention side effects, permissions, or error handling. Adequate but not thorough.

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 sentence with a parenthetical, front-loading the key behavior. Efficient and clear, though could benefit from a list-like structure for parameters.

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?

No output schema, no annotations, and only partial parameter descriptions. Missing prerequisites (e.g., molecule must be loaded) and success/error information. Adequate for basic use but lacks depth.

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 coverage is 0%, so description must compensate. It explains 2 of 5 parameters (color and style) with examples, but omits molid, material, and selection. Partially helpful but incomplete.

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

Purpose5/5

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

The description clearly states the tool adds a representation without clearing existing ones, with examples of layering. It distinguishes itself from sibling tools like set_representation and clear_representations.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly says 'without clearing existing ones', implying when to use it (to keep existing reps) and contrasting with alternatives that might clear. It does not name alternatives directly but the context is clear.

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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