When dealing with complex molecular systems, manually selecting atoms, residues, or ligands can quickly become tedious—even frustrating. If you’ve ever found yourself zooming and clicking around just to isolate one component of a protein-ligand complex, this post is for you.
Enter NSL, or the Node Specification Language, in SAMSON. NSL allows you to select molecular entities based on intelligent, customizable queries. You define what you want, and NSL finds it for you.
The pain of traditional selection
In standard workflows, selecting specific atoms or residues often requires a combination of mouse clicks and toggling visibility layers. This can be error-prone, inefficient, and almost impossible in large biomolecular systems. Now imagine needing to isolate only the non-cysteine residues in a chain of several hundred residues. Cue NSL.
What is NSL?
NSL is a simple yet powerful language that you can use within the Find command or in the Document view inside SAMSON. It helps you query and filter nodes—like atoms, residues, ligands, structural groups—based on their attributes, spatial locations, connections, and more.
You can use NSL through the Find tool in SAMSON’s interface or incorporate it into your workflow programmatically. Better yet, there’s even an AI Assistant integrated to help you generate expressions contextually.
Getting started with the Find command
Inside SAMSON, activate the Find command and type an NSL query in the search box. Hit Tab for autocomplete suggestions. Here’s an example:
|
1 |
"ALA |
Pressing Tab at this point can suggest entries like:
"ALA 22 Backbone""ALA 22""ALA 28 Side chain"
This is an easy way to quickly locate structures by name—even if you don’t remember the full name.
Common examples that can save you hours
H: selects all hydrogen atomsn.t r and not r.t CYS: selects all residues that are not cysteines"CA" within 5A of S: selects atoms named “CA” within 5Å of any sulfur atomn.t sc h S: finds side chains that contain a sulfur atom
Why it matters
You’ll save time, reduce errors, and be confident that your selection is based on precise criteria—not just visual inspection. NSL is especially helpful when setting up simulations, analyzing interactions, or preparing figures for publications.
Pro Tip: Ask the AI Assistant
Feeling hesitant about the right syntax? Use the Ask AI button in the Find tool interface. The assistant understands the current molecular document and can generate NSL expressions tailored to your structure. That’s right—you don’t have to memorize anything to get started.
To learn more about NSL and maximize your node selection workflows, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.