Molecular modeling involves frequent selection of specific atoms, residues, chains, ligands, or binding sites. This task can become tedious and error-prone, especially in complex molecular systems. Traditional selection tools involve dropdowns, checkboxes, or writing selection syntax. Not only does this impact your workflow speed, but it also breaks your focus when trying to quickly analyze or manipulate structures.
If you’re using SAMSON, there’s an easier way. With the SAMSON AI, you can now select molecular components using natural language thanks to the /select command. This lets you perform selections with simple text instructions—no need to learn a custom selection language or scroll through endless tree nodes.
Why this is useful
- Less friction: Instead of writing complex queries, just type what you mean.
- Accessibility: Great for students, new users, or anyone unfamiliar with command syntax.
- Speed: Immediate action without needing to manually browse or highlight.
How it works
The /select command in SAMSON AI allows you to describe what you want to select in plain English. Behind the scenes, SAMSON AI translates this to a query in the Node Specification Language (NSL) and applies the selection to your current molecular document.
For example, you can type any of the following in the Assistant window:
/select the binding site./select all side chains within 5 angstrom of the ligand./select all lysines in chain B.
The system understands the intent and applies very precise queries using NSL.
When this matters the most
Here are a few situations where this capability can drastically improve your workflow:
- You’re analyzing drug-like molecules and need to isolate residues within a given radius.
- You’re preparing scripts or simulations and need to highlight specific molecule parts quickly.
- You want to generate consistent selections across multiple structures without redefining them each time.
The Assistant acts like a bridge between you and complex query logic—freeing you to think about chemistry and structural biology, not syntax.
Want to go further?
Selections made this way are just the start—you can then act on them using other commands like /do (e.g., to color or transform the selection), or generate scripts with /script for reproducible workflows.
This kind of interface lowers technical barriers for new users while expanding the productivity potential of experienced modelers and developers. If you’re managing PDB structures regularly, this may be one of the simplest ways to reduce friction in your interaction with the software.
To learn more, visit the full documentation at https://documentation.samson-connect.net/users/latest/samson-ai/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.