Control PyMOL with natural language. Make molecular visualization simple and efficient.
简体中文 | English (Current)
As shown in the screenshot, you only need to describe your needs in everyday language, and the AI will directly control PyMOL to complete complex molecular visualization tasks.
This project is maintained simultaneously on GitHub and Gitee:
| Platform | URL | Recommendation |
|---|---|---|
| GitHub | https://github.com/Masterchiefm/pymol-ai-assistant | ⭐ International |
| Gitee | https://gitee.com/MasterChiefm/pymol-ai-assistant | 🇨🇳 China (Recommended) |
Tip: Users in China are recommended to use Gitee for faster and more stable download speeds.
| Feature | Description |
|---|---|
| 🤖 AI Chat | Control PyMOL with natural language, no need to memorize complex commands |
| 🌊 Streaming | Real-time display of AI thinking process and output with color distinction |
| 🔧 Tool Calling | AI can directly operate PyMOL: load structures, set styles, save images, etc. |
| ⚙️ Config Management | Support multiple API configs (SiliconFlow, OpenAI, etc.), import/export supported |
| 📋 Logging | Record all conversations and tool calls, with filtering and export |
| 🌐 Bilingual | One-click switching between Chinese/English interface, language preference auto-saved |
| 📜 Chat History | View complete chat_history JSON for debugging and analysis |
| 📦 Auto Dependencies | Automatically check and install required dependencies on installation |
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Download Plugin
- GitHub: Releases Page
- Gitee: Releases Page
- Download
pymol-ai-assistant.zip
-
Installation Steps
- Open PyMOL → Plugin → Plugin Manager
- Click "Install New Plugin"
- Select the downloaded zip file
- Restart PyMOL
-
Launch PyMOL
-
Menu bar: Plugin → AI Assistant
-
Configure API for first-time use:
- Click "⚙️ Config" button (or "⚙️ 配置" in Chinese interface)
- Add API configuration (URL, Key, Model)
- Supports SiliconFlow, OpenAI, and other OpenAI API-compatible services
-
(Optional) Click "🌐 中文" to switch to Chinese interface. Language preference is automatically saved.
API URL: https://api.siliconflow.cn/v1
Recommended Models:
- Pro/moonshotai/Kimi-K2.5 # Best overall, paid
- Pro/zai-org/GLM-4.7 # Paid
- deepseek-ai/DeepSeek-R1 # Free modelRegistration Bonus:
- Get 16 CNY voucher with invite link: https://cloud.siliconflow.cn/i/Su2ao83G
- Or visit Kimi official website for monthly plans
After configuration, type commands in the input box and press Enter to send.
| Tab | Content |
|---|---|
| 💬 Chat | Chat interaction interface |
| 📋 Logs | System logs and debug information |
| 📜 History | View complete chat_history JSON |
- 👤 User Message: Blue background, displayed on right
- 🤖 AI Message: Green background, displayed on left
- 💭 Thinking Process: Gray italic
- Formal Output: Normal text
- ⚙️ Tool Call: Orange display
- ✓ Tool Result: Green/Red status
Load PDB 1ake, select each chain and color them, display surface with transparency
What is the distance between the two residues I selected? Show me the measurement.
Rotate view 90 degrees, then save as image
Create a selection of all atoms in chain A
Execute PyMOL script /path/to/script.pml
Run command: load 1ake; show cartoon; color chain
Load and run Python script /path/to/setup.py
This project is licensed under the MIT License - see the LICENSE file for details.
Issues and Pull Requests are welcome!
If this project helps you, please consider giving it a Star ⭐!
This project was primarily developed with the assistance of AI models:
- Kimi K2.5 (Moonshot AI) - Core architecture and functionality
- GLM-4.7 (Zhipu AI) - Code optimization and feature enhancement
With the help of AI, the developer realized this powerful PyMOL intelligent plugin by describing requirements in natural language.
Made with ❤️ and AI (Kimi K2.5 & GLM-4.7)