Easily Select Helices, Strands, and Loops in Molecular Models

A common pain point for molecular modelers is the need to quickly select and manipulate secondary structure elements—like alpha helices, beta sheets, and loops—in large biomolecular systems. Whether you’re preparing a visualization, performing a simulation setup, or designing mutations, manually identifying these regions can be tedious and error-prone.

If you’re using SAMSON, there’s a more precise and automated way to handle this task using the Node Specification Language (NSL). Specifically, the residue.secondaryStructure attribute (short name: r.ss) lets you directly match residues belonging to specific types of secondary structure with a simple query.

How It Works

The r.ss attribute supports the following secondary structure classifications:

  • alpha helix: alpha, a, helix, or h
  • beta strand: beta, b, strand, or s
  • unstructured (loop): unstructured, u, loop, or l

This means instead of manually hunting for alpha helices, you can simply type:

This NSL query immediately selects all residues that are part of an alpha helix.

Need to isolate both helices and strands? Use a comma-separated list:

This selects residues in both alpha helices and beta sheets.

Typical Use Cases

This feature is useful in many practical scenarios:

  1. Visualization: Customize how different structural regions appear in your model. Highlight helices in red and strands in blue, for example.
  2. Mutagenesis: Focus mutations on specific structural elements, such as targeting loops for surface exposure modifications.
  3. Simulation preparation: Exclude flexible loops from initial minimization steps, or define collective variables based on structured domains.
  4. Validation: Quickly flag incomplete or disordered regions in experimental structures.

Thanks to NSL’s flexibility, these queries can also be combined with others for even more targeted selections. For example, the following selects only alpha helices in amino acids with a positive charge:

No Guesswork, Just Queries

With the r.ss attribute, structure-aware selections are no longer tedious. No scrolling through a structure. No coloring by hand. Just intuitive queries that get you what you need, fast.

👉 Explore the full documentation of residue.secondaryStructure to learn more about its aliases and use cases.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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