When dealing with large biomolecular systems, keeping track of the structural components—especially side chains—can be overwhelming. If you’ve ever needed to pinpoint side chains based on the number of atoms or specific elements they contain, then you know how time-consuming manual selection can be. Fortunately, SAMSON’s Node Specification Language (NSL) makes this task far more efficient.
In this post, we’ll dive into how SAMSON users can filter and analyze side chains based on atomic attributes like number of carbons, hydrogens, nitrogens, and more using NSL. This is especially useful for identifying chemically specific regions, preparing simulations, or analyzing mutation effects in protein structures.
Why Filter Side Chains?
Suppose you’re interested in finding side chains that could contribute to specific interactions based on the types or quantities of atoms they contain. For example:
- Identify potentially charged side chains with a high formal charge.
- Focus on hydrophobic side chains by finding those rich in carbon atoms.
- Analyze rotamer library candidates with a specific number of atoms.
Instead of manually browsing through residues, you can use NSL queries in SAMSON to precisely and instantly isolate what you’re looking for.
Useful Attributes for Side Chain Filtering
Here are some of the most practical attributes inherited from the structuralGroup attribute space:
sc.fc— formalCharge: useful for locating ionizable side chains.sc.nat— numberOfAtoms: total number of atoms in a side chain.sc.nC,sc.nH,sc.nN,sc.nO,sc.nS— atom counts by element.sc.ncga— numberOfCoarseGrainedAtoms: if you’re using coarse-grained models.sc.pc— partialCharge: for analyzing electrostatic properties.
Some Example Queries
You can fine-tune your selection using comparison operators. Here are some illustrative examples:
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// Find side chains with more than 8 carbon atoms sc.nC > 8 // Find side chains with formal charge between 1 and 3 sc.fc 1:3 // Find side chains with fewer than 10 atoms sc.nat < 10 // Search for side chains rich in nitrogen sc.nN >= 3 |
To use these queries, simply type them into the NSL interface in SAMSON’s selection editor. The results will update automatically—no scripting required.
Applications
- Visualization: Highlight specific side chains for presentations or publications.
- Simulation prep: Select chemically significant side chains for charge or force field tweaking.
- Structural analysis: Study patterns in residue composition or mutation results.
Whether you’re working on enzyme active sites or trying to model charged patches on a surface, this filtering method can save you time and avoid user error.
This capability is part of NSL’s broader design philosophy: empowering molecular modelers to interact more intuitively and powerfully with complex systems.
To learn more, visit the full documentation page for Side Chain Attributes: 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.