If you’re working in molecular modeling, you’ve likely found yourself repeatedly diving through hierarchies of chains, residues, and atoms to apply selections—especially when dealing with large biomolecular complexes. These selections may be necessary to analyze binding sites, investigate side chain behaviors, or prepare visualizations. While traditional selection interfaces rely on pickers or semi-complex query languages, they can slow down your workflow when things get too intricate.
This is where SAMSON AI’s /select command becomes particularly helpful. Instead of clicking through lengthy trees or crafting lines of code, you can now describe what you want in natural language, and let AI translate it into precise molecular selections.
Natural language, powerful queries
Imagine you’re analyzing a protein-ligand interaction. You want to highlight every lysine on chain B. Traditionally, that might involve filtering through the structure or writing a query script. With SAMSON AI, all you have to do is type:
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/select all lysines in chain B. |
Done. The assistant selects just what you need.
Other examples:
/select the binding site./select all side chains within 5 angstrom of the ligand.
Each of these triggers SAMSON AI’s Node Specification Language (NSL) engine under the hood, but you don’t have to write or understand the specifications yourself—unless you want to. The resulting selection query is displayed to keep things transparent, so you always know what’s going on.
When is this useful?
This kind of selection is extremely useful in many scenarios:
- Focused visualization: highlight key interaction residues quickly.
- Site-directed mutagenesis studies: select specific residues to mutate or analyze.
- Distance-based selections: define spatial neighborhoods through intuitive phrases.
- Tutorial demonstrations: guide students or colleagues through complex models easier and faster, without needing to teach them a scripting language first.
In collaborative environments, the readability of natural-language instructions also improves communication between team members who might have varying scripting skill levels.
Try it yourself
To access it, open SAMSON AI via Interface > Assistant or use the keyboard shortcut (Ctrl + 0 on Windows/Linux or Cmd + 0 on Mac). Then type /select followed by your request.
Here’s a snapshot of the Assistant in action, where a list of commands is triggered by typing /:
Overall, this capability isn’t about convenience alone—it’s about reducing the unnecessary friction that gets in the way of actual science. For complex or time-pressing analyses, cutting down on selection time gives you more room to focus on the insights that matter.
To learn more about what SAMSON AI can help you with, including other commands like /do and /script, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.