When working with complex molecular systems, visual clutter and data overload can slow researchers down. Molecular modelers often need to isolate specific subsets of structures, such as conformational paths that involve many atoms, without manually examining each one.
This is where the Node Specification Language (NSL) in SAMSON can offer a significant boost. In this blog post, we’ll focus on the numberOfAtoms attribute of path nodes—an efficient way to narrow down a search to relevant molecular paths with a controlled number of atoms. This is a practical and often overlooked tool for managing complexity in large molecular designs.
Why filter by number of atoms?
When dealing with trajectories or conformational changes in molecular simulations, not all paths are equally relevant. Some may involve just a few atoms and are uninteresting for a particular analysis, while others might capture the backbone of an entire macromolecule or complex assemblies.
Using a path-level filter based on atom count allows modelers to:
- Focus on significant structural changes involving large subunits
- Improve rendering speed by ignoring small, peripheral paths
- Automate selection criteria for scripting and workflows
How does it work in NSL?
SAMSON’s NSL provides a concise way to express queries. The path.numberOfAtoms attribute, or p.nat in short form, can be used to filter paths based on how many atoms they contain. The syntax is both readable and expressive.
Here are two common use cases:
p.nat > 100— matches all path nodes that contain more than 100 atoms.p.nat 100:200— selects paths with atom counts between 100 and 200 (inclusive).
These filters are especially useful when combined with other NSL attributes like path name (e.g., p.n "A*" and p.nat > 150), allowing fine-grained selection within large datasets.
Best practices and tips
- Use ranges when you’re not sure of the exact atom counts but have an approximate target (e.g. medium-sized conformational segments).
- Combine with logical operators (e.g.
and,not) to refine queries without having to perform multiple selection steps. - Preview matches selectively to quickly validate your filters before applying them to entire structures.
This small but practical capability helps users stay focused by pulling signal from noise. Whether you’re scripting with NSL or building automation tools within SAMSON, filtering by atom count can help you spend less time clicking and more time discovering.
To learn more about path attributes in NSL, visit the official documentation: https://documentation.samson-connect.net/users/latest/nsl/path/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net