Quickly Identify Segments by Atom or Residue Count in SAMSON

If you work with large and complex molecular systems, you’ve probably encountered the challenge of filtering specific segments based on properties like the number of atoms, residues, or atoms of certain elements. Manually evaluating these properties one by one is error-prone and inefficient, especially in dense molecular assemblies or hybrid models that mix coarse-grained and atomistic regions.

The good news is that SAMSON’s Node Specification Language (NSL) provides a clean and readable way to filter segments with precision using attributes like numberOfAtoms, numberOfResidues, or numberOfHydrogens. Understanding how to use these attributes can significantly reduce the time you spend manually inspecting or selecting segments.

Segment Attribute Filtering: A Closer Look

Within the NSL, the segment attribute space (short name: s) includes multiple useful attributes that describe key properties of segments. Let’s focus on a few that can simplify your workflow:

  • s.nr: Number of residues in the segment
  • s.nat: Total number of atoms
  • s.nH, s.nC, s.nO: Number of hydrogens, carbons, and oxygens respectively
  • s.ncga: Number of coarse-grained atoms

Examples That Make Modeling Easier

Here are a few example queries that let you filter segments based on structural properties:

  • s.nr > 130: Selects segments with more than 130 residues
  • s.nat 100:200: Filters segments containing 100 to 200 atoms
  • s.nH < 10: Finds segments with fewer than 10 hydrogen atoms
  • s.ncga > 100: Useful for identifying coarse-grained segments

These shortcuts are especially valuable when analyzing large datasets, where you may want to isolate a specific class of segments (e.g., small ligands, long protein chains, hybrid modeling regions) without browsing through a hierarchy tree manually.

Combining Filters for Enhanced Exploration

You can even combine multiple filters for powerful querying. For example:

…selects segments with more than 100 residues but fewer than 20 hydrogen atoms. This could help in detecting modified proteins or analyzing binding pockets in partially solvated systems.

When This Matters Most

Some common use cases that benefit from this filtering include:

  • Identifying segments likely to be ligands (based on small number of atoms)
  • Detecting water clusters or ions (usually low residue and atom counts)
  • Segmenting coarse-grained regions automatically during analysis
  • Getting stats on polymer segments quickly by their size and composition

Using NSL segment attribute filters is not only efficient, it scales well when working with large supramolecular systems or simulations containing thousands of segments.

To explore more available attributes and refine your filtering even further, visit the official documentation page: SAMSON NSL Segment Attributes.

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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