When exploring or comparing molecular conformations, one common challenge modelers face is identifying specific types of paths—especially based on their complexity or size. For instance, locating paths that include a large number of atoms can help identify long chains, extended molecular regions, or conformational outliers. Filtering manually can be time-consuming, especially in large systems.
Fortunately, SAMSON’s Node Specification Language (NSL) provides a simple way to define molecule selections through attribute-based queries. A very useful attribute in this context is path.numberOfAtoms, or p.nat for short. With it, you can directly select paths based on how many atoms they contain—a critical criteria when screening structural features, organizing datasets, or setting up simulations.
When is filtering by number of atoms useful?
Here are some typical use cases:
- Identifying extended conformations: Sort conformational paths by length (e.g.,
p.nat > 300) to detect unfolded or elongated states. - Filtering small fragments: Select shorter paths (e.g.,
p.nat < 10) to exclude or isolate ligands, fragments, or solvent molecules. - Targeting mid-sized conformations: Use interval filtering (e.g.,
p.nat 100:200) to find paths of a particular size range. - Bounding complexity in path analysis workflows: Quickly reduce decision space when using scripting, visualization, or pathway comparisons that are sensitive to structure size.
How to use p.nat in your selections
Start with typing your query in the filter bar within SAMSON’s selection interface. The syntax is straightforward:
p.nat > 100— select all paths with more than 100 atoms.p.nat 100:200— select all paths with between 100 and 200 atoms (inclusive).
You can combine p.nat with other NSL filters. For example:
p.nat > 50 and p.selected— select only the currently selected paths that include more than 50 atoms.
Here is a table summarizing the usage:
| Query | Description |
|---|---|
p.nat > 100 |
Select paths with more than 100 atoms |
p.nat < 50 |
Select paths with fewer than 50 atoms |
p.nat 150:300 |
Select paths with atom counts between 150 and 300 |
By mastering even just this one attribute—numberOfAtoms—you’ll be able to navigate your molecular datasets more efficiently, especially when dealing with large, multi-conformational systems.
To learn more about how to filter paths in SAMSON, visit the full documentation page: https://documentation.samson-connect.net/users/latest/nsl/path/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.