When working on simulations or structure analysis involving biomolecules or polymers, molecular modelers often deal with numerous conformations. Sifting through these to isolate the most relevant ones—such as those with a high number of atoms—can become time-consuming, especially when visual inspection isn’t enough.
If you’re using SAMSON, the good news is you don’t need to manually sort or tag everything. Using the Node Specification Language (NSL), SAMSON makes it possible to write concise queries that search for specific node properties—like the number of atoms in a given path (i.e., a conformation).
What is the path.numberOfAtoms Attribute?
The path.numberOfAtoms attribute—short name p.nat—can be used to filter nodes that represent conformations based on the number of atoms they contain.
This provides a direct and fast way to restrict your selection to conformations above or within a certain size range. This is especially useful when:
- You’re trying to isolate large or complex conformations for further analysis
- You need to discard very small fragments from a conformational scan
- You want to pre-filter for visualization or export only the relevant structures
Using p.nat in Practice
You can use the p.nat filter through the NSL interface in the Search bar or script-based filters inside SAMSON. Here are some examples and what they do:
p.nat > 100— selects paths (conformations) that contain more than 100 atoms.p.nat 100:200— selects paths that have between 100 and 200 atoms (inclusive).
If you’re already visualizing molecular data sets with hundreds (or thousands) of conformations, these filters let you interactively reduce clutter and zero in on what’s most important for your analysis. Combine this with other attributes, like p.n "A" or p.selected, to build complex yet manageable filters tailored to your project.
Why This Matters
In conformational studies, it’s common to generate large data sets automatically—whether from molecular dynamics or systematic scans. Many of these conformations may be partial, irrelevant, or not meet size criteria. The ability to filter by numberOfAtoms helps eliminate noise without modifying your data. And because you’re using the same search syntax available for all nodes in SAMSON, integrating this into your workflow is seamless. No need for external scripts or manual counting.
Instead of exporting too many conformers and then filtering them in a different tool, stay within SAMSON and target exactly what you need. 🧬
To learn more about available query options and how to combine them efficiently, check out the full documentation on the SAMSON Node Specification Language here:
https://documentation.samson-connect.net/users/latest/nsl/path/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.