Molecular modelers often spend excessive time manually navigating complex molecular documents just to select or isolate the nodes they are interested in. Whether you’re trying to highlight a ligand, isolate a group of residues, or analyze a subset of hydrogens, a more precise and efficient method is available in SAMSON: the Node Specification Language (NSL).
One standout way to use NSL is inside the Document View. Instead of scrolling endlessly through nodes, you can write a short query to instantly filter and select the nodes you’re looking for.
Save Time with NSL Filtering
SAMSON’s Document View lets you browse through a hierarchical structure of nodes (atoms, residues, chains, etc.). With many nodes and nested groups, finding what you need can become cumbersome. NSL solves this problem by letting you describe exactly what you’re searching for using a compact string.
Here’s an example: to isolate structural groups, you only need to write:
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n.t sg |
This is the short form of:
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node.type structuralGroup |
Once typed into the filter box in the Document View, press Enter and all structural groups in your document will be highlighted. No manual browsing necessary.
Don’t Know the Syntax? Ask the AI Assistant
If you’re unsure how to construct your NSL expression, SAMSON can help you with that too. By clicking the Ask AI button 
next to the filter field, the AI Assistant will suggest a query tailored to the document you’re currently working on. It’s aware of your document’s node hierarchy and proposes expressions that are immediately relevant.
Tips to Get You Started
- Select all atoms:
n.t a - Select only residues:
n.t r - Select ligands or receptors:
n.c lig, rec - Select nodes named ALA:
"ALA*"
NSL supports logical combinations too. For example, to find nodes that are residues but not Alanine:
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n.t r and not r.t ALA |
Why Use NSL in Document View?
- Precision: Select exactly what you need, even in complex structures.
- Speed: No more manual scrolling or browsing through folders.
- Reproducibility: Save your NSL queries and reuse them across sessions.
This is especially useful when dealing with large biomolecular structures or simulations where visual navigation becomes impractical.
To learn more about filtering nodes using NSL and other useful functionalities, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.