When working on complex molecular models, even seasoned researchers can experience friction: too many clicks, scattered tools, or scripting overhead just to zoom into a ligand or color-code a surface. These interruptions break focus and slow down workflows. What if you could simplify all of that with just a few words?
Enter SAMSON AI, the intelligent assistant built into SAMSON, the integrative molecular design platform. If you’ve ever opened the Assistant interface and wondered what to do next, here’s a tip: just type /.
The ‘/’ That Changes Everything
Typing / into the SAMSON AI Assistant reveals a powerful menu of commands. These aren’t ordinary chatbot prompts—they’re natural language shortcuts for performing advanced modeling tasks directly inside SAMSON.
Whether you’re analyzing binding sites, writing Python scripts, or teaching the AI to pull in external knowledge, the Assistant interprets your input intelligently. Here’s a breakdown of the available commands:
/do– Perform actions in the document (like selecting, coloring, or deleting models)./script– Generate Python code using the SAMSON API./select– Select nodes with natural language (e.g. nearby residues, specific chains)./learn– Teach SAMSON AI from an online PDF or web page./refer– Ask questions about information taught via/learn./forget– Reset everything the AI has learned.
Why It Matters
Molecular modelers often toggle between modeling tools, scripting windows, and external documentation. This mode-switching adds overhead. By integrating actions, scripting, and learning into one interface, SAMSON AI helps researchers stay focused on their modeling objective—not on the software navigation.
Consider an example where you want to clean up a structural model by removing water molecules and highlighting the binding pocket. Typing the following into the Assistant:
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/do remove water /do zoom to the binding site /select all side chains within 5 angstrom of the ligand /do color them yellow |
This sequence of interactions would have taken significantly longer with manual clicks or custom scripts. What’s notable is how intuitive and repeatable it becomes—perfect for molecular designers who work with many systems.
Visualizing the Commands
When you type / in the Assistant box, this is the menu you’ll see:
Each command comes with its own logic and flexibility. For instance, /script can generate a GUI that accepts input values for on-the-fly geometry manipulation. /learn allows the AI to digest an entire scientific article so you can refer back to it later.
A New Kind of Interface
Commands like /select and /script are designed with your modeling logic in mind. They let you work with structures the way you think about them: “side chains within 5Å”, “lysines on chain B”, or “calculate the gyration radius”—without needing to memorize function names or syntax.
If voice interaction suits your flow, SAMSON AI even understands spoken prompts like “do zoom to the active site”. Just turn on your audio output to hear confirmations, or see the Assistant act on your words immediately.
More to Explore
This layer of interaction with SAMSON is about more than convenience—it’s about accelerating molecular insight. As scientific modeling grows more complex, tools like SAMSON AI help reduce the cognitive load so researchers can focus on science.
Learn more by visiting the full documentation here: https://documentation.samson-connect.net/users/latest/samson-ai/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.