One of the most time-consuming and repetitive tasks in molecular modeling is scripting. Whether you want to automate structure manipulation, calculate properties, or build custom GUIs, scripting remains essential—but not always straightforward. For many users, the hurdles range from not remembering API syntax to needing results faster than documentation can be parsed.
Enter SAMSON AI, the intelligent assistant built into the SAMSON molecular design platform. If you’re using the Professional plan, you now have access to a GPT-5-powered assistant that can understand natural language and generate usable Python scripts with just a command. This has the potential to save hours of trial-and-error coding, especially when prototyping or quickly testing ideas in molecular models.
What does the /script command do?
The /script command tells SAMSON AI to generate a Python script based on your description. These scripts can then be executed or adapted, just like any code you’d write manually, but without the need to refer constantly to the API documentation.
Here are a few examples you can try directly in the SAMSON AI input field:
/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.
Instead of starting your script from scratch, you get a clean, readable Python script utilizing the SAMSON Python API. This is especially helpful for those who are less familiar with the syntax or want to mix SAMSON scripting with external tools like machine learning libraries or analysis frameworks.
Why this matters
Imagine working on a new ligand-receptor system, and you want to apply a simple geometric transformation to your model. Previously, you’d look up the right SAMSON API methods, write the script, test it, and debug if needed. SAMSON AI brings this process down to a single step:
/script move all atoms of the ligand up by 2 angstroms
You instantly get a ready-to-run script. This can dramatically boost productivity in early-stage modeling, preparing structures for docking, or customizing visualizations without diving deep into the API every time. It also shortens the learning curve for students or new users who want results faster.
Combining natural language with scripting power
This capability is part of a broader concept called retrieval-augmented agency, which leverages both trained language models and direct access to tools—in this case, SAMSON’s scripting API. By combining the two, you’re no longer limited to conversation: you get executable, editable code that works in your current molecular model.
Whether you’re tweaking atom colors for visualization or calculating structural descriptors, SAMSON AI can provide a playable script in seconds, helping you focus more on the modeling goal than on the syntax.
To explore the full set of SAMSON AI features, visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.