When working with complex molecular systems, molecular modelers often deal with multiple conformations of a structure. Whether you’re filtering simulated outputs, preparing structures for further analysis, or needing to isolate specific states from a pool, being able to quickly find conformations based on the number of atoms is a common and recurring need.
This task can become tedious if you’re manually sifting through large datasets. Fortunately, the SAMSON platform offers a powerful way to query structural data using the Node Specification Language (NSL)—and in particular, the conformation.numberOfAtoms attribute lets you select conformations based on atom count using simple and expressive queries.
Filtering by atom count with co.nat
The attribute conformation.numberOfAtoms (or simply co.nat) is specifically designed for this task. With NSL, you can create filters in seconds. Here are a few useful examples:
co.nat > 100: Matches all conformations with more than 100 atoms.co.nat 100:200: Matches conformations with 100 to 200 atoms.
These expressions allow for fast, on-the-fly filtering, removing the need to write custom scripts or export data to external tools. This has wide-ranging applications across modeling workflows:
- Isolating small-molecule conformations from larger assemblies
- Focusing on ligands or cofactors in protein-ligand complexes
- Identifying problematic conformations (e.g., unexpectedly large or small)
Combining filters for more precision
You can also combine the co.nat filter with other attributes for more targeted selection. For instance:
co.nat > 50 and co.selected: Selects conformations with more than 50 atoms that are currently selected in the viewport.co.nat 80:120 and co.n "Ligand*": Filters for conformations with 80–120 atoms that have names starting with “Ligand”.
This level of detail makes SAMSON’s NSL ideal for visual analysis and scripting alike.
Why this matters
Especially when working on drug-like molecules, transition state ensembles, or conformational searches, being able to easily filter by atom count directly within the modeling environment saves time and avoids extra steps. These small time savings accumulate during daily work and reduce the friction of exploratory modeling.
Advanced users can integrate such filters into Python scripts inside SAMSON, while beginners benefit from immediately applicable examples.
More on NSL
If you’re unfamiliar with NSL, it’s SAMSON’s dedicated language for querying molecular nodes. In the context of conformations, it focuses on relevant attributes such as name, selectionFlag, and atom count.
To explore all available conformation attributes, visit the full documentation page: 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.