If you’ve ever spent too long trying to manually select specific atoms, residues, or molecular components for your simulation or visualization, you’re not alone. This is a common challenge among molecular modelers and structural biologists. Fortunately, the Node Specification Language (NSL) in SAMSON makes advanced selections precise, efficient, and reproducible.
What is NSL?
The Node Specification Language (NSL) is SAMSON’s query language designed to describe selections of nodes—atoms, residues, chains, structures, and more. NSL allows you to express complex selections using a concise, readable syntax. This becomes incredibly useful when working with large systems, repeating operations across similar components, or preparing customized visualization and analysis workflows.
Why Use NSL?
- Speed: Selecting nodes with a textual query is much faster than manual selection using the mouse.
- Reproducibility: You can save and reuse NSL queries across sessions and projects.
- Precision: NSL captures selections that would otherwise be impractical or prone to error using the GUI alone.
Basic Syntax Examples
Here are a few examples to get you started:
all— Selects all nodes in the document.protein— Selects all protein residues.resname == "ATP"— Selects all residues with the name ATP.chainID == "A" && resSeq > 50— Selects all residues in chain A with sequence numbers greater than 50.element == "C"— Selects all carbon atoms.
Combining Expressions
NSL supports logical operators like && (and), || (or), and ! (not). For example:
protein && !backbone— Selects all side chain atoms in a protein.resname == "LIG" || resname == "ATP"— Selects all residues named LIG or ATP.
Use Cases
Here are some practical examples any modeler might run into:
- Visualization: Color all ligand atoms differently from the protein to highlight interactions.
- Simulation Setup: Select solvent molecules to exclude them or apply constraints.
- Analysis: Identify all atoms near a specific residue with a distance-based selection macro.
Tips
- Preview Selections: In SAMSON, you can test queries and preview the selected nodes before applying changes.
- Documentation: Always refer to the syntax guide for operators, property names, and supported node types.
If you’ve struggled with selections before, spend a few minutes learning NSL syntax—you’ll quickly find your workflow more streamlined and error-resistant.
To learn more about NSL queries and integrate them into your daily use of SAMSON, visit the official documentation page: https://documentation.samson-connect.net/users/latest/references/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.