How to Quickly Find Backbone Groups with Specific Atomic Compositions in SAMSON

If you’ve ever needed to search for backbone components with a particular atomic makeup in complex molecular models, you know how tedious this process can become. Whether you’re filtering for small ligands, labile functional groups, or large structural chunks, doing it manually slows down workflows and increases the chances of overlooking important structures.

The Node Specification Language (NSL) in SAMSON offers a powerful solution: fine-grained attribute filtering for backbone nodes. This lets you quickly target, visualize, or modify molecular backbones based on atomic composition—number of carbons, hydrogens, nitrogens, and more.

This guide focuses on a practical subset of attributes in the backbone NSL space: atomic count filters. These allow you to rapidly spot structurally relevant groups by applying human-readable queries.

Why This Matters for Molecular Modelers

Imagine wanting to locate all peptide backbones with fewer than 10 carbon atoms, which could correspond to small loops or fragments. Or perhaps you’re designing coarse-grained models and want to verify all backbones include fewer than 100 coarse-grained atoms. Rather than counting atoms manually or switching tools, you can type one line in SAMSON using NSL.

Examples of Atomic Count Queries

The following attributes are available for backbone nodes in SAMSON’s NSL:

nat — numberOfAtoms
nC — numberOfCarbons
nH — numberOfHydrogens
nN — numberOfNitrogens
nO — numberOfOxygens
nS — numberOfSulfurs
ncga — numberOfCoarseGrainedAtoms

You can use simple comparison or range operators. Here are some actionable example queries:

bb.nC < 10 → Backbone groups with fewer than 10 carbon atoms
bb.nH 20:30 → Backbone groups with 20–30 hydrogen atoms
bb.nO > 5 → Backbone groups rich in oxygen (e.g., possible polar regions)
bb.ncga < 500 → Coarse-grained backbones under 500 atoms

Combining Filters

Multiple filters can be combined for more refined searches. For instance, to find backbones that are rich in oxygen and simultaneously poor in sulfur:

bb.nO &gt; 8 and bb.nS &lt; 2

1	bb.nO > 8 and bb.nS < 2

A Shortcut for Insight

Attribute filters like these are essential when navigating large systems. You might use them to:

Identify mismodeled structures during model cleaning
Screen for chemically interesting features
Quickly isolate specific groups for visualization or simulation

Contextual Use: Partial Charges

Need to include electrostatic insight? You can also filter on partialCharge (pc):

bb.pc &gt; 1.5

1	bb.pc > 1.5

This lets you combine geometric or elemental filtering with physicochemical properties.

While short and flexible, the NSL syntax in SAMSON can be a major timesaver once you get used to it. Even better, all these filters integrate seamlessly into visual workflows for clear insights.

To learn more about backbone filtering using node attributes, visit the full documentation here: https://documentation.samson-connect.net/users/latest/nsl/backbone/

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