For many molecular modelers, automating repetitive tasks or customizing workflows often means writing Python scripts. But when it comes to integrating scripting into powerful modeling environments like SAMSON, the learning curve can feel steep—especially if you’re not a Python expert.
The good news is that SAMSON AI includes a simple way to bridge this gap. With its /script command, SAMSON AI reads your natural language prompts and generates Python scripts tailored to your request. Whether you’re aligning molecules, analyzing protein trajectories, or building your own molecular design tool, this feature offers a fast and intuitive path to scripting—even for users with minimal programming experience.
Why scripting matters
As projects grow more complex, manual processes often become bottlenecks. Custom scripts allow you to:
- Automate repetitive workflows (like batch-processing conformations or customizing representations)
- Extract or compute properties over trajectories
- Build custom GUIs for specialized inputs
But if you’ve ever hesitated to dive into scripting, the /script command in SAMSON AI is a helpful starting point.
How it works
To use the /script feature, open SAMSON AI in your workspace (Interface > Assistant or Ctrl+0 / Cmd+0) and type a plain-English description of what you want to automate or build, preceded by /script.
For example:
/script select all atoms and translate them in the z direction by 1 angstrom./script create a GUI that lets me enter a distance in angstrom, with a 'Move' button./script compute the gyration radius of the receptor.
The AI will respond with a Python script using the SAMSON Python API. You can then copy, modify, and run the code directly within the scripting environment in SAMSON.
What makes this useful
The value here isn’t just about saving time. It also lies in turning vague ideas into concrete starting points. You no longer need to memorize function names or call signatures—the AI does that for you. Even better, you can iteratively refine your script by requesting enhancements using follow-up prompts, like:
/script Now color the selected atoms red.
Furthermore, since it runs on the GPT-5 model in the Professional plan, the AI can understand fairly complex language and make useful suggestions, reducing the need to constantly reference documentation.
Combining with external Python libraries
Once you have your generated script, you’re free to integrate it with your own Python libraries—e.g., NumPy for numerical analysis or matplotlib for plotting. This makes SAMSON AI not just a command assistant, but also a powerful entry point to fully customized modeling pipelines.
To explore this feature and try your own prompts, check the full documentation page on the /script command here: SAMSON AI Script Command.
To learn more about SAMSON AI, its other commands, and how it can improve your workflow, visit the official documentation page: https://documentation.samson-connect.net/users/latest/samson-ai/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.