Molecular modelers often find themselves repeating the same visualization or selection tasks across dozens of projects. Coloring surfaces, hiding water molecules, zooming to binding sites — these small actions can accumulate into a frustratingly time-consuming part of an otherwise creative workflow.
Fortunately, SAMSON AI—the intelligent assistant built into the SAMSON platform—offers a way to shortcut these repetitive actions using natural language. In this blog post, we’ll take a look at the /do command, a feature that lets you execute various SAMSON actions just by typing or saying simple instructions.
What is the /do Command?
The /do command lets you interact with SAMSON using ordinary language. Instead of digging through menus or browsing toolbars, you can type commands like:
/do zoom to the binding site./do remove water./do select the ligand and apply a licorice model./do erase all surfaces./do select the gaussian surface and make it light blue.
These tasks, which typically require multiple clicks, can now be done with a one-liner—and even faster if you use your voice.
Why It Matters
While no single action may consume much time, the total effort spent repeating them across projects can be significant. For researchers analyzing multiple protein-ligand complexes, quickly jumping to a binding site or stripping away water molecules without navigating the interface may save hours of manual work—freeing more time for scientific thinking rather than software operation.
In teaching or demonstration settings, the time savings become even more valuable. Instructors can prepare workflows in advance or demonstrate them live, with students learning how to control a full-featured molecular design platform using natural language alone. It also serves as a stepping stone to developing more advanced interactions, such as those involving scripting or learned documents.
See It in Action
If you prefer voice-based interaction, SAMSON AI also supports speaking commands. You can watch a quick video example of this feature below:
This voice-driven control is part of what’s known as retrieval-augmented agency (RAA), where the underlying knowledge about SAMSON allows the assistant to perform actions directly in your molecular design environment.
How to Get Started
You can open SAMSON AI from the SAMSON interface by going to Interface > Assistant, or using the keyboard shortcut:
- On Windows and Linux: Ctrl + 0
- On macOS: Cmd + 0
Then, in the input box, type /do followed by your command. To see a full list of available options, simply type / to show command suggestions.
Whether you’re working on complex projects or teaching basic structure exploration, /do is a simple way to reclaim your time and streamline your daily tasks.
To learn more about SAMSON AI and its full capabilities, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.