Quickly Filter Side Chains by Atomic Composition in SAMSON

When working with large molecular systems, pinning down specific structural features like the number of atoms in side chains can be tricky—especially when you’re searching across thousands of residues. This is a common pain point for molecular modelers who want to focus on functionally or chemically distinct side chains without spending hours manually filtering through data.

Fortunately, SAMSON’s Node Specification Language (NSL) offers a solution. If you’re focusing on side chains, the sideChain attribute space (abbreviated as sc) provides a way to filter nodes based on atomic features like the number of carbon, hydrogen, nitrogen, oxygen, sulfur atoms, and more. This can significantly streamline your modeling and analysis workflow.

Why atomic composition filtering matters

Imagine you’re searching for side chains that are rich in sulfur for studying disulfide bonds, or side chains with a small number of atoms for spotting potential druggable pockets. Manually identifying these features would be tedious. But with NSL, you can use concise and readable queries.

Examples of powerful filters

Here are some example filters you can use in SAMSON’s Query panel or scripting environment with NSL:

  • sc.nC > 3 – Select side chains with more than 3 carbon atoms
  • sc.nS – Highlight all side chains that contain sulfur atoms
  • sc.nH 5:10 – Match side chains with between 5 and 10 hydrogen atoms
  • sc.fc != 0 – Find side chains with a formal charge

This level of filtering helps reduce visual clutter and isolate chemically meaningful features quickly. These attributes are not standalone—they’re inherited mostly from the structuralGroup attribute space, enabling a consistent language across different structural types.

List of Available Atomic Filters

Here is a summary of atomic composition-related attributes that you can use with sc queries:

  • fc – formalCharge: integers (e.g., sc.fc -1)
  • nat – numberOfAtoms: total number of atoms in the side chain (e.g., sc.nat < 20)
  • nC – numberOfCarbons: number of carbon atoms
  • nH – numberOfHydrogens: number of hydrogen atoms
  • nN – numberOfNitrogens
  • nO – numberOfOxygens
  • nS – numberOfSulfurs
  • ncga – numberOfCoarseGrainedAtoms: useful in coarse-grained models (e.g., sc.ncga > 0)
  • pc – partialCharge: floating point values (e.g., sc.pc > 1.5 or sc.pc 0.8:1.2)

These filters are fully documented with usage examples in the official documentation. They’re essential tools you can rely on to automate selection tasks and accelerate your modeling workflows.

Smarter selections, better productivity

By using NSL to target specific atomic composition criteria, you can guide your visualizations, simulations, and even scripting tasks more precisely and quickly. This is particularly useful when setting up simulations, validating structures, or preparing publication images.

To learn more about side chain attributes and see all available query options, visit the official SAMSON documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get it from SAMSON Connect.

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