# MCPymol

> Use this tool when you need to interact with molecular structures using natural language, enabling efficient structure loading, analysis, and exploration. MCPymol solves problems in protein research and visualization by allowing users to input natural language commands and outputting corresponding PyMOL actions and visualizations. It is ideal for use cases where intuitive and automated protein structure analysis is required, accepting text inputs and producing graphical outputs.

Canonical page: https://skillsregistry.net/skills/chemrich-mcpymol  
JSON: https://api.skillsregistry.net/v1/skills/chemrich-mcpymol

## Description

A Model Context Protocol server that lets you drive PyMOL with natural language, enabling structure loading, analytical views, measurements, and protein exploration through AI assistants.

## Trust

- **Trust score (0–1):** 0.47
- **Verification tier:** scanned
- **Last scanned:** 2026-08-31

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** other
- **Updated:** 2026-08-31

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/fujhhy0hoz)
- **Repository:** <https://github.com/chemrich/MCPymol>

## 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": "chemrich-mcpymol"
    }
  }
}
```

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

---
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