When working with complex molecular structures, identifying and isolating regions of interest—binding sites, side chains, specific residues across chains—can be time-consuming, especially across large molecular systems. Traditionally, this requires either manual inspection or scripting in specialized query languages.
SAMSON AI, the assistant built into the SAMSON molecular design platform, offers a helpful alternative: natural language selection of nodes and molecular substructures.
Why this matters
Whether you’re setting up a molecular dynamics simulation, preparing a visualization, or performing a custom analysis with a scripting engine, selecting the right atoms or residues is one of the first steps. Manual selection might be feasible for small molecules, but quickly becomes inefficient in large structures or ensembles.
SAMSON AI’s /select command lets you describe what you want in plain English, and the assistant handles the rest. This makes it easier to stay focused on your scientific goals instead of spending time on syntax details or repetitive manual clicking.
How it works
Under the hood, when you send a /select query, SAMSON AI translates your natural language input into the Node Specification Language (NSL)—SAMSON’s internal query system. It then executes the query to highlight the corresponding selection in your current document.
You’ll also see the NSL translation of your query, which is useful if you want to reuse it in a script or refine it further.
Examples in practice
Here are a few examples of natural language queries that SAMSON AI understands:
/select the binding site./select all side chains within 5 angstrom of the ligand./select all lysines in chain B.
These are not just text matches—SAMSON AI interprets biochemical concepts and relationships to generate an appropriate NSL expression. It also highlights the selected components directly in the molecular view, saving time for repetitive tasks.
Combining with other features
The power of /select becomes even more useful when combined with other SAMSON AI commands, like:
/do zoom to the selection– to center the camera on your selection/do apply a Van der Waals model– to change the render style immediately/script– to convert selections into scripted workflows
This capability accelerates exploratory work and makes SAMSON more accessible for users who may not be familiar with existing selection languages or APIs.
Try it yourself
To start using this feature, open SAMSON AI via Interface > Assistant or use the keyboard shortcut Ctrl + 0 on Windows/Linux, or Cmd + 0 on macOS.
Type /select followed by your query, and watch how your molecules respond.
For more details and examples, visit the SAMSON AI documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download the platform at https://www.samson-connect.net.