For many molecular modelers, selecting specific parts of large molecular structures—residues in a chain, atoms in a binding site, or side chains near a ligand—can be a recurring bottleneck. Traditional selection involves manually clicking through models or crafting complex queries in a specialized syntax. Errors are easy to make, and the process is often time-consuming.
This is where SAMSON AI can help. If you’re a molecular modeler using the SAMSON platform, you’ll be interested to know that SAMSON AI includes a command called /select that allows you to make selections simply by writing (or saying) what you want. That’s right—you can use natural language like “select all lysines in chain B” and let the AI handle the rest.
Why this matters
Selections form the basis for most operations in molecular modeling: you visualize, compute, modify, and measure based on what you’ve selected. When models get large and complex, the ability to quickly and precisely select the parts you’re interested in—without memorizing syntax or navigating menus—can save hours. It also reduces the chance of human error from manual selections or incorrect commands.
Natural language to the rescue
The /select command translates plain English into precise queries using SAMSON’s Node Specification Language (NSL), and then executes the selection immediately. Here are a few examples of what it can understand:
/select the binding site/select all side chains within 5 angstrom of the ligand/select all lysines in chain B
Each of these would require much more effort through a graphical interface or scripting, but with SAMSON AI, they’re one-liners.
Seeing the result visually
Once the selection is made, the corresponding molecular elements are highlighted in the SAMSON document. Moreover, SAMSON AI shows the generated NSL query, providing a useful learning opportunity: you don’t only get the result, you also get to better understand the underlying selection syntax.
This is particularly useful for new users who are gradually learning the NSL query system but still want to be productive and precise today. You can also copy-paste or adapt the generated queries later on, combining the best of both AI-guided and manual approaches.
When precision counts
An underrated benefit of using AI-assisted selection is replicability. Instead of repeating manual steps for each dataset, you can reuse plain-language prompts or generated codes in your workflow documentation so that colleagues—or your future self—can reproduce the same selection quickly.
Getting started
To use /select in SAMSON AI, open the Assistant window via Interface > Assistant or use the Ctrl + 0 (Windows/Linux) or Cmd + 0 (Mac) shortcut. Then, type your query prefixed by /select, and let the assistant do the work.
You can learn more about node selection and the Node Specification Language (NSL) here.
To explore more about the capabilities of SAMSON AI and how it integrates with selections in your workflows, visit the SAMSON AI documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.