For molecular modelers working with complex biomolecular systems or nanomaterials, scripting in Python opens up powerful pathways for automation, reproducibility, and customization. But not everyone finds it easy to write Python code—especially when trying to interact with a domain-specific interface like SAMSON’s. That’s where the /script command in SAMSON AI becomes genuinely helpful.
SAMSON AI’s /script command is designed to bridge the gap between natural language and scripting. Instead of digging through documentation or looking for code snippets online, you simply tell the AI what you want—using your own words—and it generates the Python code for you.
Why this matters: a look at the pain point
Many molecular modelers often have great ideas they want to test. Maybe you want to compute the radius of gyration of a protein or apply a custom transformation to atoms. However, unless you’re already fluent with SAMSON’s Python API, implementing even small tweaks might bog you down in syntax and error-checking.
In other words: great scientific intent often crashes into real-world scripting barriers. Instead of getting derailed, SAMSON AI’s /script command gives you a shortcut: describe it in plain English, and the AI helps translate that into SAMSON-ready Python code.
Examples that might save you time
With the /script command, you can:
- Move selected atoms:
/script select all atoms and translate them in the z direction by 1 angstrom. - Build interactive tools:
/script create a GUI that lets me enter a distance in angstrom, with a 'Move' button. - Do structural analysis:
/script compute the gyration radius of the receptor.
Every generated script can be further modified, reused, or extended as your project evolves.
Beyond coding: what this unlocks
If you’re teaching students, prototyping a method, or simply trying to speed up tedious interactions, the /script command helps create a smoother path between what you want to do and the Python code that does it. It complements the SAMSON Python API, giving you a conversational on-ramp to a powerful programming environment. If you’re new to Python, it can help you learn through examples. And if you’re an experienced coder, it can save time for routine parts of the job.
Once a script is generated, you remain in control. You can inspect, edit, or integrate the generated code into your own workflows. And since you don’t need to leave the SAMSON environment or switch back and forth between the documentation and the script editor, the development loop becomes faster and more seamless.
How to try it
To use the /script command in SAMSON AI:
- Open the Assistant from Interface > Assistant or use the shortcut Ctrl + 0 (or Cmd + 0 on Mac).
- Type
/scriptfollowed by your request in plain English.
This feature is available as part of the Professional plan, which includes GPT-5 integration.
To see the full set of capabilities and more script examples, visit the full documentation page here.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.