When working with complex biomolecular structures, identifying specific subgroups—like side chains with a particular number of atoms or elements—can be time-consuming. Whether you’re analyzing reactive sites, searching for hydrophobic residues, or customizing visual representations, targeted selection is essential for efficient molecular modeling.
If you’ve used SAMSON before, you know that the Node Specification Language (NSL) allows powerful and precise selection operations. But did you know that you can use NSL to filter side chains based on their elemental composition or formal charge using simple, compact expressions?
Why Elemental Filtering Matters
Say you’re investigating potential binding pockets and want to identify all side chains rich in nitrogen or oxygen atoms. Manually reviewing hundreds of residues can be exhausting. NSL makes this process almost instantaneous.
A Look at the Attributes
SAMSON exposes the following attributes in the sideChain attribute space (short name: sc), inherited from the structuralGroup space:
sc.nC: number of carbon atomssc.nH: number of hydrogen atomssc.nN: number of nitrogen atomssc.nO: number of oxygen atomssc.nS: number of sulfur atomssc.fc: formal charge
Examples You Can Use Right Now
Want to find side chains with high nitrogen counts?
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sc.nN > 2 |
Looking for side chains with a formal charge between 1 and 3?
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sc.fc 1:3 |
Select all side chains with fewer than 10 carbons:
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sc.nC < 10 |
These queries can be used directly in SAMSON’s advanced selection tools, letting you quickly isolate and manipulate the specific groups you need. Whether you’re scripting operations or just visually inspecting, this hands-off filtering saves time and avoids manual errors.
Combining Filters
You can combine multiple attribute conditions to get even more specific:
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sc.nN > 1 and sc.nO > 1 |
This selects side chains that have more than one nitrogen and more than one oxygen atom—useful for identifying polar or charged residues in proteins.
Partial Charge Considerations
When partial charge data is available, NSL allows filtering based on that as well:
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sc.pc > 1.5 |
This enables users to select side chains with high partial charge values, which can influence interaction behavior in simulations or docking studies.
Compatible with Selection Workflows
All these expressions integrate seamlessly with SAMSON’s visual inspection and editing workflows—once selected, side chains can be highlighted, hidden, exported, or modified as needed.
Efficient selection is just one part of effective molecular design. But mastering NSL’s side chain filtering capabilities gives you a flexible and precise tool for exploring structure and function in large systems.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/nsl/sideChain/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.