# PyMOL-MCP

> PyMOL-MCP — jonathan6620-pymol-mcp. Use this tool when you need to analyze and visualize molecular structures through conversational interactions, leveraging natural language inputs to explore and understand complex biological systems. PyMOL-MCP connects PyMOL to Claude AI, enabling seamless integration of molecular visualization and analysis capabilities. It accepts natural language queries as input and outputs interactive 3D visualizations and analysis results, ideal for structural biologists and researchers seeking intuitive and efficient molecular insights.

Canonical page: https://skillsregistry.net/skills/jonathan6620-pymol-mcp  
JSON: https://api.skillsregistry.net/v1/skills/jonathan6620-pymol-mcp

## Description

Connects PyMOL to Claude AI for conversational structural biology, molecular visualization, and analysis through natural language.

## Trust

- **Trust score (0–1):** 0.37
- **Verification tier:** scanned
- **Last scanned:** 2026-08-29

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-08-29

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/jblufb79hz)
- **Repository:** <https://github.com/jonathan6620/pymol-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "jonathan6620-pymol-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/jonathan6620-pymol-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/jonathan6620-pymol-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt