When working with molecular systems in SAMSON, researchers often deal with complex models containing numerous conformations. A common challenge during analysis is identifying conformations based on specific structural features—such as the number of atoms. For instance, in simulations involving conformational ensembles, users may want to isolate structures that are over a certain size or within a particular atom count range to study molecular stability, perform clustering, or prepare inputs for further simulations.
This is where the Node Specification Language (NSL) comes into play. NSL allows you to filter conformations efficiently based on numerous attributes. One particularly useful attribute is numberOfAtoms, accessible via the short-hand co.nat. By mastering this small but powerful filter, you can save time and streamline your modeling workflow—even when working with large molecular systems.
Why Filter by Number of Atoms?
Examining a dataset of conformations typically involves focusing on a subset with meaningful characteristics. Size—measured here as the number of atoms—is often a good proxy for identifying structural completeness, detecting unusual conformations, or narrowing down candidates for visualization and analysis.
Using co.nat
The conformation.numberOfAtoms attribute (short name: co.nat) matches conformations with a specific number of atoms. Here are typical usage examples:
co.nat > 100: selects conformations with more than 100 atoms.co.nat 100:200: selects conformations with atom counts between 100 and 200, inclusive.
Here’s what this looks like in action inside a query within SAMSON Search:
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co.nat > 150 |
This returns all conformations in your document that contain more than 150 atoms. Pair it with other logical operators or attributes to further refine your selection.
This feature is very useful when coping with hundreds—or even thousands—of conformations, especially when you’re trying to exclude fragments or partial conformations that may arise during automatic generation or filtering steps.
Common Use Cases
- Trajectory analysis: Select stable states above a certain size threshold for further processing or visualization.
- Filtering noisy data: Quickly exclude incomplete or overly small conformations generated during molecular docking or minimization pipelines.
- Preparation for simulations: Pick conformations of consistent size for batch running in GROMACS or other engines.
Things to Keep in Mind
Note that co.nat is specific to the conformation attribute space, so always prefix your query with co.. This avoids potential mismatches and keeps your queries clear and specific.
To learn more, check the original documentation page here: https://documentation.samson-connect.net/users/latest/nsl/conformation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.