Filtering Backbone Structures Using NSL: A Practical Guide for Molecular Modelers

If you’re working with complex molecular systems, you likely face the challenge of isolating specific structural groups or backbones based on their properties. Whether you’re performing coarse-grained modeling, refining selection in visualizations, or analyzing structural consistency, manually identifying and filtering backbone fragments can quickly become a bottleneck.

The Node Specification Language (NSL) in SAMSON offers a solution through powerful attribute-based filtering. With NSL, you can query molecular models for structural information using precise conditions. In this blog post, we focus on using backbone attributes within the NSL framework to help you work more efficiently with molecular backbones.

Why Focus on Backbones?

Backbone structures often form the scaffold of biological macromolecules like proteins and nucleic acids. Understanding and manipulating backbone components is fundamental in areas like protein folding analysis, molecular dynamics, and drug binding studies. Using NSL, you can streamline backbone filtering with syntax that’s both flexible and intuitive.

The Attribute Space

The backbone attribute space (short name: s) includes attributes inherited from two other attribute groups:

• node: general attributes, such as visible or selected
• structuralGroup: chemistry-specific attributes, like numberOfAtoms or formalCharge

All of these can be accessed using the bb prefix in your NSL queries. Here are some scenarios molecular modelers often encounter—and how to solve them.

Common Use Cases with Examples

1. Select Backbones Based on Atomic Count

If you’re analyzing only mid-sized groups of atoms, you may want to filter by the number of atoms in the backbone:

This selects backbone structures that contain between 100 and 200 atoms.

2. Identify Highly Charged Backbones

Backbones with a high formalCharge may be structurally or functionally important:

3. Highlight Backbones with Many Carbons

Useful when you’re exploring variations in aliphatic chains or hydrophobic cores.

4. Visualize Only Visible Backbones

If you’ve got a lot of structural clutter, this can clean up your view:

Or hide them explicitly:

5. Filtering Based on Partial Charge

This returns backbones with partial charges in a specific range—a handy tool for electrostatic analysis or preparing QM/MM regions.

Flexible and Combinable Queries

You can combine multiple filters using logical operators. For example, to find visible backbones with more than 200 atoms:

Refining Your Model Efficiently

Filtering backbone structures using NSL can drastically reduce manual inspection time and make your modeling workflow more scalable. Whether you’re setting up an ensemble refinement, visualizing charged regions, or cleaning up dynamic trajectories, NSL’s attribute syntax gives you rich control without scripting.

To explore all available attributes and see more examples, visit the full documentation page on backbone attributes in NSL.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.