When working with complex molecular systems, molecular modelers often face the challenge of navigating and managing large numbers of conformations. Some conformations may only contain a few atoms, others might represent larger fragments or complete molecules. If you’re trying to focus on biologically relevant parts—like full protein chains or ligand candidates—filtering by atom count can help you eliminate noise and significantly speed up your workflow.
Thanks to conformation attributes available in SAMSON’s Node Specification Language (NSL), this task can be done with a concise and human-readable syntax. In this post, we’ll walk through how to use the numberOfAtoms attribute efficiently to isolate conformations based on their atomic size.
Why filter by number of atoms?
Often during molecular modeling, we import or generate structures that include extra data—solvent molecules, stray hydrogen atoms, or partial fragments from simulations. In such cases:
- You may want to focus only on conformations that are likely to be full molecules (e.g., >100 atoms).
- You might need to analyze conformations within certain size ranges (e.g., 100 to 200 atoms).
- You’ll want to avoid manual inspection of every conformation node, especially in large systems.
How to do it in NSL
In SAMSON’s NSL, conformations have a specific attribute space named conformation, or simply co for short. One valuable attribute in this space is numberOfAtoms, with short name nat.
Selecting conformations with more than 100 atoms:
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co.nat > 100 |
This command matches all conformations that have more than 100 atoms.
Selecting conformations with 100 to 200 atoms:
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co.nat 100:200 |
This matches all conformations that include between 100 and 200 atoms. The range notation is concise and very readable.
Use cases in molecular modeling
This can be especially helpful in the following situations:
- After an MD simulation: filtering meaningful conformations based on size.
- During ligand screening: exclude partial structures or fragments.
- In visual analysis: reduce clutter by auto-selecting a subset of interest before visualization.
Pairing this attribute with other filters such as conformation name (co.n) or selection flags (co.sf) gives even more nuanced control over what you focus on in a model.
Pro tip: Combine selections!
You can create very powerful expressions using NSL logic. For example:
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co.nat > 100 and co.sf |
This selects conformations with more than 100 atoms that are flagged for selection.
By using these kinds of filters, you’ll spend less time on manual sorting and more time on meaningful analysis.
Learn more in the NSL conformation attributes documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.