# PyMOL

> Use this tool when you need to analyze protein structures, examine binding sites, or create publication-quality molecular visualizations. It provides interactive protein structure analysis through a comprehensive set of tools, including loading structures from PDB files and manipulating visualizations. The tool accepts natural language instructions and outputs high-quality images, making it suitable for researchers and educators who require robust molecular visualization capabilities.

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

## Description

The PyMOL MCP server provides a bridge between Claude and the PyMOL molecular visualization software, enabling interactive protein structure analysis through a comprehensive set of tools. Built with Python using the FastMCP framework, it offers capabilities for loading structures from PDB files, manipulating visualizations with different representations and colors, measuring molecular distances and angles, and rendering high-quality images. The implementation includes robust error handling and logging, making it particularly valuable for researchers and educators who need to analyze protein structures, examine binding sites, or create publication-quality molecular visualizations through natural language instructions.

## 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/gdamitha-pymol)
- **Repository:** <https://github.com/gdamitha/mcp_claude>

## 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": "gdamitha-pymol"
    }
  }
}
```

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