Molecular modelers working with complex systems often need to focus on specific subsets of molecules, such as backbone groups with particular atomic compositions. Manually identifying these substructures can be time-consuming and prone to error—especially in large biomolecular systems.
Fortunately, the Node Specification Language (NSL) in SAMSON provides a powerful way to filter and select molecular components based on a range of attributes. In this post, we’ll explore how to query backbone groups based on their atomic composition using attributes like numberOfAtoms, numberOfCarbons, numberOfHydrogens, and others. These features allow modelers to sift through structural data more efficiently and focus attention where it’s most needed.
Why focus on atom counts?
In structural biology and chemistry, different functional regions have characteristic atomic compositions. For instance, detecting regions with unusually high nitrogen or sulfur content can help identify active sites or structural motifs. Atom count filters are invaluable when analyzing structural groups across proteins, nucleic acids, or synthetic systems.
Backbone group attributes for compositional analysis
In NSL, the attribute space backbone (or its short form s) refers to backbone nodes detected in molecular structures. The following table summarizes attributes available for querying by atom count (all inherited from the structuralGroup attribute space):
| Attribute | Short Name | Type | Example Query |
|---|---|---|---|
| numberOfAtoms | nat |
Integer | bb.nat < 1000 |
| numberOfCarbons | nC |
Integer | bb.nC 10:20 |
| numberOfHydrogens | nH |
Integer | bb.nH > 5 |
| numberOfNitrogens | nN |
Integer | bb.nN 2:4 |
| numberOfOxygens | nO |
Integer | bb.nO < 5 |
| numberOfSulfurs | nS |
Integer | bb.nS 1 |
| numberOfCoarseGrainedAtoms | ncga |
Integer | bb.ncga 100:200 |
| partialCharge | pc |
Float | bb.pc > 1.5 |
Example use cases
- Filter structures with moderate oxygen content:
bb.nO 5:10helps you isolate backbone groups with a specific oxygen range, which may correlate with polar functional motifs. - Identify small backbone groups:
bb.nat < 50is useful when targeting small structural domains or fragments for further analysis. - Hunt for sulfur clusters: Use
bb.nS > 2to find areas rich in sulfur, often key to metal-binding or disulfide linkages in proteins. - Detect charged backbones:
bb.pc 1.5:2.0can help locate groups with significantly high partial charge.
Tips for combining filters
One of the strengths of NSL is the ability to combine conditions using logical operators. For example, to find backbone nodes with low atom counts but significant charge:
|
1 |
bb.nat < 100 and bb.pc > 1.0 |
This flexibility can streamline complex workflows, especially when preparing systems for simulation, docking, or visualization.
To explore additional filters and syntax, visit the full documentation on backbone attributes in NSL.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.