# PyMOL

> Use this tool when you need to visualize and manipulate molecular structures, especially for structural biology workflows, drug design, and protein engineering tasks. It enables AI assistants to execute commands, retrieve structural information, and edit PDB files through a bidirectional communication bridge with PyMOL. The integration accepts JSON-RPC requests and outputs molecular visualizations and structural data, making it ideal for interactive molecular analysis and design.

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

## Description

PyMOL-Claude Integration enables AI assistants to visualize and manipulate molecular structures in PyMOL through a bidirectional communication bridge. Developed by Andre Watson, it implements both a PyMOL plugin that starts an MCP-compatible server and a standalone MCP server script that handles JSON-RPC requests from Claude. The integration allows Claude to execute PyMOL commands, retrieve structural information, edit PDB files, and manage molecular visualizations directly within conversations, making it particularly valuable for structural biology workflows, drug design, and protein engineering tasks that benefit from interactive molecular visualization.

## Trust

- **Trust score (0–1):** 0.30
- **Verification tier:** unverified
- **Last scanned:** 2026-09-02

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** productivity
- **Updated:** 2026-09-02

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/nanogenomic-pymol)
- **Repository:** <https://github.com/nanogenomic/molai/tree/HEAD/FINAL>

## 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": "nanogenomic-pymol"
    }
  }
}
```

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