Working on complex molecular systems often means juggling dozens of visualization states, selections, and scripts in SAMSON. Setting up a view, applying the right model to a ligand, or cleaning up water molecules can take up valuable time—especially when repeated across multiple projects or sessions.
What if you could just tell your modeling platform what you want, using natural language, and have it done instantly? That’s where SAMSON AI commands come in. With simple command-line prompts like /do, /select, or /script, you can cut through the interface and speak directly to the functionality you need.
What Are SAMSON AI Commands?
SAMSON AI includes a built-in assistant based on GPT-5 (in the Professional plan) which understands special commands you can type for rapid molecular manipulation, scripting, and learning from external data. To bring up the SAMSON AI, just go to Interface > Assistant or press Ctrl + 0 (Windows/Linux) or Cmd + 0 (Mac).
Typing / in the Assistant’s input field will suggest available commands, including:
/do: execute actions in the document/script: generate Python scripts/select: select model elements with natural language/learn,/refer,/forget: manage external knowledge sources
Common Use Cases for Faster Workflows
1. Instantly Clean Up Your Workspace
Instead of manually deselecting and hiding unwanted elements, just type:
|
1 |
/do remove water |
Need to reset your view to zoom in on the active site?
|
1 |
/do zoom to the binding site |
2. Apply Custom Visualization Styles
If you’re preparing figures or just navigating the structure:
|
1 |
/do select the ligand and apply a licorice model |
|
1 |
/do select the gaussian surface and make it light blue |
3. Teach SAMSON AI What to Know
Use /learn to teach SAMSON AI from a paper or web page, like a research article or data sheet:
|
1 |
/learn https://www.biorxiv.org/content/10.1101/2022.08.03.502585v2.full.pdf |
Later, ask direct questions about the content with /refer:
|
1 |
/refer What is the molecular structure of the compound described? |
Bonus: Speak Instead of Type
Prefer using your voice? Just say your command aloud, like “do zoom to the selection”. Here’s a video showcasing this in action:
Why It Matters
For molecular modelers working on tight deadlines or repetitive visualization and preparation tasks, using AI-driven commands is a highly effective way to reduce clicks and avoid context switching. These commands extend SAMSON as a retrieval-augmented agent (RAA), combining structured information with powerful execution capabilities, directly from your natural language input.
Explore the full list of commands and examples by visiting the SAMSON AI documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.