Many molecular modelers spend significant time navigating menus, remembering shortcuts, and writing scripts to perform everyday tasks: visualizing surfaces, modifying representations, or selecting atom groups. While flexibility is appreciated, the friction can add up—especially when switching between modeling tools and workflows.
Imagine performing these tasks simply by speaking or typing natural commands. That’s the promise behind SAMSON AI’s /do command: an intelligent assistant that listens—quite literally—and carries out your requests within the SAMSON molecular design platform.
Introducing the /do Command
SAMSON AI includes a collection of commands, but one of the most immediate time-savers is /do. You can type it—or say the word “do” out loud—and follow it with a natural language instruction.
Examples include:
/do zoom to the binding site/do select the ligand and apply a licorice model/do remove water/do erase all surfaces/do select the gaussian surface and make it light blue
These may seem straightforward—but what makes this special is the fact that you don’t need to know how to perform these edits manually. AI parses your request and interfaces with SAMSON’s internal command system to get it done.
You Can Also Speak
If you prefer voice over typing, SAMSON AI allows you to speak the command. Just say “do” followed by your instruction. The assistant interprets the phrase and executes it.
This is especially helpful while focusing on 3D visualization or interacting with results from simulations—less time spent navigating, more time understanding structures.
Behind the Scenes
Technically speaking, this feature is an example of what’s called retrieval-augmented agency (RAA). In simple terms, SAMSON AI draws on its built-in knowledge of your molecular system and integrates it with the SAMSON platform’s internal commands. It’s not just interpreting your command; it’s executing actions within a live molecular model.
Here’s a visual example of the command interface in action:
When Speed Matters
Anyone who’s worked with molecular systems knows the frustration of repetitive layer management or representation tweaking. The /do command is especially useful for:
- Quickly cleaning up a loaded structure (e.g., removing water or ions)
- Focusing on a specific site (e.g., ligand, active site)
- Changing visual styles to prepare figures or presentations
- Simplifying model interactions when teaching or explaining structures to others
Getting Started
You can activate SAMSON AI from the menu at Interface > Assistant, or use the shortcut:
- Ctrl+0 on Windows/Linux
- Cmd+0 on Mac
Then type or say your command—starting with “do”—and let the assistant handle it from there.
To explore this feature further, check out the full documentation at https://documentation.samson-connect.net/users/latest/samson-ai/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.