pymol-claude-plugin

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pymol-claude-plugin

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Claude AI plugin for PyMOL to control PyMOL with plain English

pymol-claude-plugin 최신버젼 다운로드

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// repository documentation

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# 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
```

---

## Requirements

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

---

## 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.

---

### Can't find the Plugin Manager?

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

**Mac / Linux:**
```bash
mkdir -p ~/.pymol/startup/
cp pymol_claude_plugin.py ~/.pymol/startup/
```

Then restart PyMOL.

---

## 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 |

---

## 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.

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