# ChimeraX MCP Server

> Use this tool when you need to control and interact with 3D protein structure visualizations using natural language commands. It enables editing and analysis of protein structures in UCSF ChimeraX through MCP clients, solving problems of complex visualization and analysis workflows. Ideal for bioinformatics and structural biology applications, it accepts natural language inputs and outputs visualized protein structures and analysis results.

Canonical page: https://skillsregistry.net/skills/mahynotch-chimerax-mcp  
JSON: https://api.skillsregistry.net/v1/skills/mahynotch-chimerax-mcp

## Description

Enables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.

## Trust

- **Trust score (0–1):** 0.68
- **Verification tier:** scanned
- **Last scanned:** 2026-09-01

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-09-01

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/ph9e8nypgf)
- **Repository:** <https://github.com/mahynotch/chimerax-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": "mahynotch-chimerax-mcp"
    }
  }
}
```

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