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vmd-hydrate-mcp

vmd-hydrate-mcp

by wjgoarxiv
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Local

render

Render molecular structures headlessly using CPU Tachyon to produce a PNG image.

Instructions

Render the current view of a loaded molecule headlessly (CPU Tachyon) and return a PNG image. Resolution is capped for safety.

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": "render"
  }
}

Input Schema

NameRequiredDescriptionDefault
molidYes
widthNo
heightNo

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.0

TDQS

B3.4/5.0
Behavior3/5

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

Discloses headless CPU Tachyon rendering and resolution cap, but does not explain side effects (e.g., state changes), error conditions (e.g., no molecule loaded), or performance implications.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Two concise sentences that provide essential information without redundancy or extraneous details.

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?

Mentions output format (PNG) but lacks details on response structure, molid semantics (though clear from context), and does not address potential errors or edge cases. Adequate but incomplete for a render tool with no output schema.

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?

With 0% schema description coverage, the description should explain parameters but does not. Only parameter names and defaults are inferable from the schema.

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?

Clearly states the action (render), resource (current view of loaded molecule), and output (PNG image). Distinguishes from sibling render_cages.

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 on when to use or not use this tool, no prerequisites mentioned (e.g., molecule must be loaded), and no comparison to alternatives like render_cages or other visualization tools.

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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