If you’ve ever tried to manually click your way through a complex molecular model just to select a few specific atoms, chains, or residues, you know how tedious and error-prone it can be. The process becomes even harder when dealing with massive biomolecular systems, where locating every carbon atom within 5 angstroms of a specific residue becomes an afternoon project on its own.
Good news: in SAMSON, you can skip the clicks entirely thanks to the Node Specification Language (NSL).
What is NSL and Why Should You Care?
NSL is a powerful text-based language that lets you select molecular structures based on their properties. Instead of clicking on each atom or dragging a selection box and hoping for the best, you can enter a small NSL query to automatically select just what you need — nothing more, nothing less.
Use Case: Selecting Node Sets with the Find Command
The Find command in SAMSON lets users enter NSL expressions directly into a search box to instantly select matching nodes: atoms, residues, structural groups, and more. Just open the Find tool and type something like:
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H linking O |
This selects all hydrogen atoms that are bonded to oxygen atoms. It’s that simple — no picking, no guesswork.
Need to check for atoms that are far from a residue of interest? Use a proximity query:
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n.t a beyond 5A of "GLN 2" |
Want a list of atoms within a specific spatial range? Try something like:
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a.x -1nm:1nm |
The flexibility is enormous — and once you learn a few expressions, you’ll be able to target nodes precisely without searching through the model manually.
Make It Even Faster with Tab Completion
Typing long strings? SAMSON supports context-sensitive auto-completion. Start typing a node name (e.g., "ALA) and press Tab. You’ll get a list of matching nodes like:
"ALA 22 Backbone""ALA 28"
This reduces typos and speeds up selection considerably.
Let the AI Help You
Still unsure how to write your NSL query? Use the Ask AI option next to the selection box. The built-in AI Assistant knows your document’s structure and can help generate NSL expressions tailored for your model.
More Than Keywords: Logical and Topological Operators
NSL lets you combine selectors with logical operators:
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n.t r and not r.t ALA |
This selects all non-alanine residues.
You can even chain operations to find structural groups with certain atoms, such as:
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n.t sc having S |
This returns all side chains that contain sulfur atoms.
Conclusion
Mastering even a small subset of NSL can transform the way molecular modelers work in SAMSON. It accelerates workflows, removes manual bottlenecks, and ensures precision in selection — which is critical whether you’re modifying structures, creating visuals, or setting up simulations.
To learn more, visit the full Node Specification Language documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON from https://www.samson-connect.net.