Claude AI Plugin for PyMOL

Control PyMOL with plain English using Claude AI.

fetch 1hsg and show the protein as cartoon, color by chain, and show the ligand as sticks

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Requirements

• PyMOL (conda, official installer, or Schrödinger)
• An Anthropic API key — get one at console.anthropic.com (pay-per-use, no subscription required)

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Installation

1. Download pymol_claude_plugin.py from this repository.

2. Install the plugin via the PyMOL Plugin Manager:

Plugin > Plugin Manager > Install New Plugin > Choose file…

Select pymol_claude_plugin.py, accept the suggested directory, and click OK.

3. Restart PyMOL.

The plugin will automatically install its dependencies on first launch.

4. Open the chat window — type claude_chat in the PyMOL command line or press F2.

5. Enter your API key when prompted. It will be saved and never asked again.

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Can't find the Plugin Manager?

If your PyMOL doesn't have a Plugin menu, copy the file manually via terminal:

Mac / Linux:

mkdir -p ~/.pymol/startup/
cp pymol_claude_plugin.py ~/.pymol/startup/

Then restart PyMOL.

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Usage

Open the chat window:

claude_chat

Or press F2. Type your request and press Enter — Claude figures out the PyMOL commands, runs them, and reports what it did. The window stays open for follow-up questions.

Example requests

• fetch 1abc and show it as cartoon colored by chain
• color all residues within 5 angstroms of the ligand as red sticks
• align my two structures and tell me the RMSD
• select all lysine residues and show them as spheres
• what secondary structure elements does this protein have?
• save a PNG screenshot to my Desktop

Commands

PyMOL command	What it does
claude_chat	Open the persistent chat window
claude_stop	Cancel a running query
claude_reset	Clear conversation history (start fresh)
claude_save	Save the chat log as an HTML file

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Tips

• Claude remembers the conversation within a session — say "now color the ligand yellow" without repeating context.
• Type claude_reset to start a new topic from scratch.