When modeling complex molecular systems, selecting exactly the right atoms, residues, or chains can get tedious. Even with powerful selection tools, the process often involves clicking through multiple menus or remembering specific selection syntaxes. This becomes especially frustrating when you want to isolate a group like “all lysines in chain B” or “side chains within 5 Å of the ligand.”
With SAMSON AI, a new assistant built into the SAMSON molecular design platform, you can now make selections using natural language. This blog post introduces the /select command, which lets you describe in plain English what you want to highlight—without writing code or navigating complex GUI options.
Natural Language + Selection = Faster Modeling
The /select command allows you to express your intent using natural language. SAMSON AI converts your request into the platform’s internal Node Specification Language (NSL) and executes the selection for you. This means you still benefit from the precision of SAMSON’s core tools—but with simpler input.
Here are a few examples you can try:
/select the binding site/select all side chains within 5 angstrom of the ligand/select all lysines in chain B
What’s helpful is that SAMSON AI doesn’t just “do” the selection—it also shows the NSL query it understood. This offers a transparent interface where you can both validate and learn from the AI’s interpretation of your prompt.
Why This Matters
In practice, selection is often the very first step toward major modeling operations: computing properties, rendering surfaces, graphing interactions—or simply cleaning up your working document. Being able to do this quickly and precisely makes modeling faster and reduces errors.
For example, you might be working on a ligand docking paper and want to visualize specific residue environments. Instead of going through chains and residue menus individually, it’s now possible to say:
/select all residues within 6 angstrom of the ligand
And immediately proceed to render or analyze them. The use of natural language also helps in collaborative environments, especially when sharing documents with new users or during live sessions with others who might not know SAMSON’s selection syntax.
Where to Find It
Open SAMSON AI via Interface > Assistant, or with the shortcut Ctrl+0 on Windows and Linux, and Cmd+0 on Mac.
Type /select in the Assistant input area, followed by your natural language instruction. Once you try it, you’ll likely find yourself switching less between menus and moving more rapidly through your workflow.
To see all available commands and options, type / in the Assistant. This will show a list of supported actions directly inside the Assistant window:
Learn more about the /select command and other SAMSON AI capabilities in the full documentation here: 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.