If you spend a significant portion of your day exploring molecular models, you’ve likely lost time navigating complex menus, toggling panels, or trying to remember tool names. This friction breaks flow and adds an unnecessary cognitive load. With SAMSON AI, there’s now a much more intuitive and fluid way to interact with your molecular models.
Instead of clicking through nested menus or remembering complex sequences of shortcuts, you can just… tell SAMSON AI what you want to do.
Introducing the /do Command
SAMSON AI includes a set of natural language commands that make it possible to perform common (and not-so-common) tasks simply by typing in a message. One of the most useful of these is the /do command.
It allows molecular modelers to carry out visual and structural manipulations with simple instructions. No scripting required, no extensive menu search. Just type (or say!) what you want:
/do zoom to the binding site./do select the ligand and apply a licorice model./do remove water./do erase all surfaces.
Speaking of saying commands—you can even use your voice. This makes live model presentations or collaborative sessions easier and smoother. In real scenarios, this is particularly helpful when guiding students or presenting in meetings.
Why This Solves a Real Pain Point
Traditional GUI-based interactions can be inefficient, especially when you’re deep into structural analysis or setting up simulations. For example, removing solvent molecules or focusing on a binding site can take multiple clicks and require being familiar with several UI components. SAMSON AI significantly reduces this friction.
By abstracting away the interface complexity and letting you engage with your model in plain English (or even just speaking), SAMSON AI improves both productivity and accessibility—especially for users who are new to the SAMSON platform.
This is especially useful when you’re multitasking—running simulations, analyzing trajectories, taking notes—in any of these cases, simplicity and speed help maintain momentum.
Visual Example
Here’s what the command experience looks like inside the assistant’s interface:
Bonus: Retrieval-Augmented Agency (RAA)
SAMSON AI doesn’t just take your commands and apply fixed rules. It uses a technique known as retrieval-augmented agency (RAA), where the system has access to internal knowledge of SAMSON and its extensions. This means your natural language prompts are interpreted with context—and result in actual actions that make sense for your projects.
How to Open the Assistant
You can bring up SAMSON AI anytime via Interface > Assistant or using the keyboard shortcut:
- On Windows or Linux: Ctrl + 0
- On macOS: Cmd + 0
This capability can be especially useful in teaching environments or during collaborative research, when quick demonstrations or adjustments are needed.
Learn More
To discover more commands like /script, /select, and others, visit the full documentation:
https://documentation.samson-connect.net/users/latest/samson-ai/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.