When working with complex molecular systems, selecting specific parts of a structure can quickly become tedious—especially when using traditional selection tools or manual inspection. Whether you’re preparing a simulation, cleaning a structure, or analyzing binding sites, precise and efficient selection is key. In SAMSON, an integrative molecular design platform, this process has been made more intuitive through its AI assistant: SAMSON AI.
A particularly useful feature of SAMSON AI is its ability to understand natural language queries for selecting molecular regions using the /select command.
Why this matters
Manually selecting by atom IDs, residue types, or coordinates can be both time-consuming and error-prone, especially across long sessions or multiple structures. Smart selection with natural language greatly simplifies tasks by allowing scientists to describe exactly what they need—just like they would to a colleague.
With /select, SAMSON AI interprets your request and highlights the relevant parts of your model using its built-in Node Specification Language (NSL), which users can optionally reuse or tweak manually for more advanced queries.
How it works
You can type your queries into SAMSON AI’s input interface by beginning with /select. Here are a few examples of things you can do:
/select the binding site./select all side chains within 5 angstrom of the ligand./select all lysines in chain B.
In each case, SAMSON AI parses your request, generates the appropriate selection using NSL in the background, and applies it to your structure.
Why this is different
Compared to GUI-based workflows or script-based solutions, this method provides a quick and accessible way to filter models without needing to know syntax or navigate multiple selection menus.
Behind the scenes, SAMSON AI integrates its understanding of molecular structure with its knowledge of the SAMSON environment. While the selections are powered by NSL, the user never needs to see that syntax unless they want to—which opens up the software to more casual or non-programming users.
Put it into practice
Here’s a typical workflow where this functionality really shines:
- Load a protein-ligand system into SAMSON.
- Type
/select all residues within 6 angstroms of the ligandto inspect or modify the binding pocket. - The selection appears in real time—you could then visualize it, change representation (e.g., to licorice or cartoon), or apply a calculation just to the selected region.
Combined with other commands like /do for visualization and /script for automation, the /select command is a small but powerful enhancement to anyone doing structural modeling, drug design, or complex system analysis.
Learn more
To learn more about features and matching AI commands, visit the official SAMSON AI documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.