When working on large biomolecular systems or designing nanostructures, researchers often face a common problem: how to quickly select the molecular conformations that matter most without having to navigate through dozens—or even hundreds—of possibilities. Knowing which conformations are worth analyzing further can save hours of work and improve clarity when visualizing or simulating your system.
SAMSON’s Node Specification Language (NSL) offers a concise way to query and filter parts of your molecular models. One particularly useful use case is filtering conformations based on the number of atoms they contain. This may sound simple, but when you’re sorting through a complex system built from multiple fragments and conformers, this tool becomes a lifesaver.
Why care about the number of atoms?
A conformation’s size can be indicative of its complexity, relevance, or simply whether it falls into a category you’re interested in—say, higher-mass conformations for docking studies or small ones for fragment-based drug design. NSL provides the numberOfAtoms attribute to make this selection straightforward.
How it works
The co.nat attribute (short for conformation.numberOfAtoms) allows you to find conformations with specific atom counts. It’s part of the conformation attribute set within NSL and directly targets conformation nodes in your model.
For example:
co.nat > 100finds conformations with more than 100 atoms.co.nat 100:200selects conformations that have between 100 and 200 atoms, inclusive.
Let’s say you’re analyzing a system formed by dozens of docked ligands. You suspect that some of the docked poses are incomplete or smaller fragments generated during the simulation. Instead of sifting through each conformation manually, you can run a quick NSL query like co.nat > 150 to focus only on conformations that likely represent full ligand poses.
Additional filtering: combine with names or selection states
What makes NSL powerful is that you aren’t limited to filtering by a single attribute. For instance, if you’re only interested in large conformations that are currently selected in the viewport, you can combine the number of atoms with the selected attribute:
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co.selected and co.nat > 150 |
Or perhaps you’ve given meaningful names to your conformations and want to extract a few that fall into a specific category and exceed a certain size:
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co.n "Ligand*" and co.nat > 100 |
These kinds of query combinations are especially useful when preparing reports, submitting selections for further refinement, or running batch simulations.
Conclusion
By using co.nat in NSL, you can streamline your workflow and reduce the cognitive and visual overload of managing large molecular models. Whether you’re working with small molecules, protein conformations, or hybrid nanostructures, selecting what you need—based on size—has never been easier.
Learn more by diving into the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.