When working with complex molecular systems, researchers and modelers often generate large numbers of conformations — possible arrangements of atoms in 3D space — during simulations and structure exploration. One common challenge is quickly identifying conformations of interest, especially when thousands are present. The ability to filter these based on specific attributes, such as how many atoms they contain, can save hours of manual inspection.
In SAMSON, the Node Specification Language (NSL) provides a precise way to query and filter molecular entities — including conformations — based on their attributes. A particularly useful capability is filtering conformations by their atom count using the conformation.numberOfAtoms attribute (short name: co.nat).
Why filter by atom count?
Let’s say you’re refining docking results or comparing the stability of different protonation states. Some of these conformations might include extra water molecules, ligands, or partial structures. Their atom counts can differ significantly, and filtering out anomalies helps you focus on structurally relevant models.
Filtering by atom count in NSL
The syntax for filtering is intuitive. To access the number of atoms attribute, you use:
co.nat— short forconformation.numberOfAtoms
You can then apply numerical expressions or ranges. Here are some useful examples:
co.nat > 100— Selects conformations with more than 100 atoms.co.nat 100:200— Matches conformations with 100 to 200 atoms inclusive.
These queries help you focus on a specific subset of your data, whether you’re analyzing protein-ligand complexes or clustering molecular dynamics results.
What does this look like in practice?
Imagine you’ve performed flexible docking that generated 1,000 different conformations. If you notice that most meaningful poses contain between 120 and 150 atoms but the output includes everything from 30-atom fragments to large 200-atom assemblies, try:
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co.nat 120:150 |
This gives you a precise view of the results that match your expectations — a small step that improves analysis clarity and efficiency.
Combining filters
You can also combine co.nat with other conformation attributes, such as name or selection flags. For instance:
co.nat > 100 and co.selected— Selects large conformations that are also currently selected in your workspace.co.nat < 90 and not co.sf— Finds small conformations without a selection flag.
Combining these filters unlocks flexible and expressive queries, especially when handling complex molecular scenes with many conformations and fragments.
To explore the full list of attributes for conformations, including how to match names, selection flags, and more:
Explore the full conformation NSL documentation →
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.