When working with complex molecular systems, filtering large datasets to focus on specific structures can be time-consuming. For instance, identifying all conformations with a certain number of atoms might involve manual inspection or scripting — tedious or error-prone steps for many modelers.
SAMSON’s Node Specification Language (NSL) provides a clean solution. In particular, the conformation attribute space lets you directly query attributes like the number of atoms in each conformation node. If you’re trying to focus your analysis on a subset of conformations based on structural size — e.g., to study molecules larger than a certain threshold or within a specific range — this approach can save significant time and reduce noise in your modeling tasks.
How to Filter by Number of Atoms
The numberOfAtoms attribute, accessible via conformation.numberOfAtoms or its short form co.nat, allows you to match conformations based on the number of atoms they contain. Here’s how it works:
co.nat > 100– Selects conformations with more than 100 atoms.co.nat 100:200– Matches conformations whose atom counts fall between 100 and 200 (inclusive).
This simple syntax becomes incredibly useful in large systems: instead of sifting through a list of conformations manually, you can instantly select only those you want to examine or pass on for simulation.
Typical Use Cases
- Filtering for simulations: You might only want to simulate conformations with at least a certain number of atoms to reduce edge effects or increase physical relevance.
- Comparing similar-sized structures: When studying variations across conformations, holding the size constant can make comparisons more meaningful.
- Cleaning data: Eliminate trivial conformations (e.g., those with few atoms) that result from segmentation or incorrect file import.
Combining with Other NSL Attributes
The co.nat filter can be combined with other attributes in the NSL system. For example:
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co.nat > 100 and co.selected |
This selects conformations with more than 100 atoms that are also selected in the interface.
Getting Accurate and Reproducible Workflows
Because this capability is query-based and not dependent on manual selection, your workflows become more reproducible. You can easily share queries with collaborators or re-run them later over updated systems.
Try It Yourself
To start using co.nat and other conformation attributes in your own project, open the Selection window in SAMSON, switch to the Node Specification Language (NSL) field, and enter your query. Results will instantly highlight conformations matching your criteria.
Learn more in the official documentation here: https://documentation.samson-connect.net/users/latest/nsl/conformation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.