When working with complex molecular systems, it’s easy to feel overwhelmed by the sheer number of paths, residues, or chains in a structure. Whether you’re studying protein folding or evaluating ligand binding, pinpointing relevant fragments fast is key to staying productive 🧪. Molecular modelers often encounter a simple but frustrating problem: how to efficiently filter paths by their size?
If you’re using SAMSON, the integrative platform for molecular design, here’s something you may not have tried yet: using the numberOfAtoms attribute in the path attribute space of the Node Specification Language (NSL).
Why filter by atom count?
Imagine you’re working with a macromolecular complex imported from a PDB file. You might want to:
- Analyze only those polypeptides or polymers that are substantial in length.
- Ignore solvent molecules or other small components automatically.
- Focus on a biological assembly’s key regions without manual selection.
Instead of clicking chains one by one, NSL lets you search by specifying atom count directly. Here’s how.
Using numberOfAtoms in the path attribute space
The path.numberOfAtoms attribute, abbreviated as p.nat, enables you to match paths with a specific number of atoms.
Examples:
p.nat > 100— returns all paths with more than 100 atoms.p.nat 100:200— matches paths with atom count between 100 and 200.
These queries operate on what’s called the path attribute space (p). When you combine them with other filters like name (p.n) or selected, you can build powerful queries to rapidly interact with complex molecular data sets.
Common use cases
Let’s say you’ve imported a molecular complex and want to exclude all ligands and water molecules. You could use:
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p.nat > 50 |
This immediately hides small molecule fragments typically smaller in size.
Or, you know you’re looking for something mid-sized, say a small peptide. Try:
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p.nat 75:125 |
That gives you just what you’re looking for, without scrolling through the document view manually.
Limitations and tips
Keep in mind that atom count is not always a direct indicator of biological relevance. Small functional sites can be missed if you’re too strict with your filters. Also, always double-check the node types if you want to be more specific (e.g., filter only backbone atoms or specific bonds).
Where to find it
You can use the NSL queries directly inside SAMSON’s selection bar or as scripting filters. Combine them with visual workflows to speed up structure preparation, editing, or data analysis.
To learn more, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.