Quickly Filter Molecular Side Chains by Atom Type in SAMSON

When dealing with large biomolecular models, pinpointing specific side chains with certain atomic compositions can be tedious and time-consuming. SAMSON’s Node Specification Language (NSL) provides a concise way to filter and select these molecular entities efficiently.

Whether you’re preparing systems for analysis, visualization, or simulation, you often need to isolate side chains based on their makeup—for example, finding all side chains with a large number of carbon atoms, or selecting only those containing a specific number of oxygen or nitrogen atoms. This is particularly useful when analyzing hydrophobic or polar side chains, studying charge distributions, or preparing functionalization strategies.

What Side Chain Attributes Can You Query?

SAMSON allows you to use sc to refer to the side chain attribute space.
The following numerical attributes are available to query:

  • sc.nat – Number of atoms
  • sc.nC – Number of carbon atoms
  • sc.nH – Number of hydrogen atoms
  • sc.nN – Number of nitrogen atoms
  • sc.nO – Number of oxygen atoms
  • sc.nS – Number of sulfur atoms
  • sc.ncga – Number of coarse-grained atoms
  • sc.fc – Formal charge
  • sc.pc – Partial charge

Examples You Can Use Right Away

Here are several examples of how to specify queries to select certain side chains:

  • Find side chains with high carbon content (e.g., hydrophobic regions):
    sc.nC > 10
  • Select side chains with low hydrogen count:
    sc.nH < 5
  • Filter side chains by oxygen content:
    sc.nO 2:4 (between 2 and 4 oxygen atoms)
  • Highlight charged side chains:
    sc.fc > 0
  • Identify partially charged side chains:
    sc.pc 1.0:2.0

Why This Matters

Combinatorial queries like sc.nC > 5 and sc.nH < 10 and sc.fc 0 allow you to extract chemically relevant groups with minimal effort. This streamlines workflows in drug design, protein engineering, and nanomaterials research.

Rather than manually inspecting residues, this approach gives you consistent, reproducible selections—ideal for scripting, automation, and visual exploration. You’ll not only save time but improve the quality and consistency of your molecular modeling tasks.

Using these meaningful, property-specific filters can help you:

  • Refine large biological structures to areas of interest
  • Analyze molecular interactions in a targeted way
  • Preprocess systems for simulation or machine learning

To explore the complete list of attributes and learn how to integrate them efficiently into your workflows, visit the full documentation at 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.

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