Every molecular modeler has experienced it: the repetitive tasks that slow you down—selecting residues, hiding surfaces, zooming into a binding site. While necessary, these routines often eat up time you’d rather spend diving into molecular insights. If you’ve ever wished for a faster way to handle these actions without digging into menus, SAMSON AI offers a surprisingly efficient solution: the /do command.
Available in the Assistant interface of SAMSON (via Interface > Assistant or the Ctrl+0 / Cmd+0 shortcut), this command is designed to automate frequently used actions in plain language. Whether you want to hide all surfaces or recolor part of your model, you don’t have to look for the right menu item—you can just type your instruction.
What is /do?
The /do command in SAMSON AI lets users perform document actions using simple instructions. Instead of navigating through multi-step menus, you communicate directly with SAMSON AI and watch the platform carry out your request almost instantly.
Examples of Tasks You Can Automate
/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.
Essentially, any action you’d normally perform through SAMSON’s interface can be executed more quickly—or even combined into a sequence—using this command.
Why Is This Useful?
This can become a significant time-saver if you’re working with multiple molecular systems or exploring variations in visualization for presentations or publications. Here are a few practical scenarios where /do shines:
- Teaching or demonstrating: Need to show student groups how to highlight a binding site or change a representation style? With the
/docommand, you can do it in seconds without pausing to hunt through menus. - Exploratory analysis: As you tune parameters or test hypotheses,
/dospeeds up workflow by eliminating interface friction. - Consistency: If you want to apply the same steps across multiple structures, scripting isn’t your only option—use the same
/docommands repeatedly across documents.
Bonus: It Works with Voice
If speaking is more convenient, SAMSON AI can respond to voice commands like “do remove water”—as long as your system settings allow voice input. This enhances accessibility and can be particularly beneficial in collaborative or live-demo settings.
Ready to Try It Out?
To start using the /do command, open SAMSON’s Assistant and simply type /do followed by your instruction. The assistant will autocomplete options if you’re not sure what to type.
This feature is available in all versions of SAMSON AI, but note that the AI is based on GPT-5 in the Professional plan, so responses may differ in quality based on your plan.
For more examples and usage details, refer to the official SAMSON AI documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.