# Molecule Visualization (ChimeraX, PyMOL)

> Use this tool when you need to visualize and manipulate molecular structures, or automate tasks in PyMOL and ChimeraX. It solves problems in scientific workflows by providing a programmatic interface to open, execute commands, and save images of molecular structures. The tool accepts commands and molecule data as input and outputs images and visualization results, making it ideal for use cases where molecular visualization and analysis are required.

Canonical page: https://skillsregistry.net/skills/chatmol-molecule-visualization  
JSON: https://api.skillsregistry.net/v1/skills/chatmol-molecule-visualization

## Description

The molecule-mcp server provides a bridge between AI assistants and molecular visualization software, enabling interaction with PyMol and ChimeraX through the Model Context Protocol. It offers tools to open visualization software, execute commands directly in these applications, and save images of molecular structures. The implementation uses FastMCP to expose these capabilities as tools that can be called programmatically, making it valuable for scientific workflows where molecular visualization and manipulation are needed without leaving the conversation interface.

## Trust

- **Trust score (0–1):** 0.97
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** media
- **Updated:** 2026-09-28

## Source

- **Source listing:** [PulseMCP](https://www.pulsemcp.com/servers/chatmol-molecule-visualization)
- **Repository:** <https://github.com/chatmol/molecule-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": "chatmol-molecule-visualization"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/chatmol-molecule-visualization` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/chatmol-molecule-visualization/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