When studying large molecular systems, zooming in on relevant structural groups is essential. Whether you’re analyzing protein backbones, coarse-grained models, or complex supramolecular assemblies, being able to filter groups of atoms based on structural attributes saves considerable time and helps focus your analysis.
In SAMSON’s Node Specification Language (NSL), you can easily filter backbone elements using attributes such as numberOfAtoms, numberOfCarbons, and even partialCharge. This offers a practical way to select only the parts of your model you’re interested in—cleanly and reproducibly.
The Pain: Too Much Structure, Too Little Focus
Let’s say you are working on a molecular system with multiple polymers chained together, and you want to analyze or visualize only the fragments that have a specific number of carbon atoms. Doing this manually can quickly become tedious and error-prone. Also, large coarse-grained models or simulations might create thousands of elements, many of which aren’t relevant to your current objective.
NSL provides a way to solve this by allowing you to write concise expressions like:
bb.nC < 10— selects all backbones with fewer than 10 carbon atomsbb.nat 100:200— filters backbones that have between 100 and 200 atomsbb.pc > 1.5— finds backbones with a partial charge greater than 1.5
This is especially useful for automatically isolating structurally significant regions, creating selections for visualization, or preparing subsets for further simulation.
Quick Reference to Backbone Structural Attributes
| Attribute | Short Name | Value Type | Example |
|---|---|---|---|
| numberOfAtoms | nat |
integer | bb.nat < 1000 |
| numberOfCarbons | nC |
integer | bb.nC < 10 |
| numberOfHydrogens | nH |
integer | bb.nH 10:20 |
| partialCharge | pc |
float | bb.pc > 1.5 |
| numberOfCoarseGrainedAtoms | ncga |
integer | bb.ncga 100:200 |
Why It Matters
Rather than sifting through lists of groups or manually selecting atoms, you can write clear, compact filters that define what you want to see. This capability is ideal for:
- Focusing on specific molecular fragments
- Automating selections for scripts or workflows
- Cleaning up visualizations by hiding irrelevant regions
For those working in cheminformatics, drug design, or material science, being able to search and manipulate structural information at scale is a core productivity tool. Even better, this system allows regex-like filtering via wildcard strings (for names), and numeric ranges or inequality expressions for attributed values.
Conclusion
If you’ve ever wanted a smarter way to focus on parts of your molecular model in SAMSON, using numerical and boolean filters on backbone attributes can make a big difference. Instead of hunting down elements manually, let NSL do the work for you.
To learn more about backbone attributes in the Node Specification Language, visit the original documentation page: https://documentation.samson-connect.net/users/latest/nsl/backbone/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.