Identifying large biomolecular segments quickly can save time and reduce errors, especially during molecular editing, visualization, or simulation prep. Whether you’re selecting protein domains, isolating specific chains, or filtering data before analysis, there’s a faster way with SAMSON’s Node Specification Language (NSL).
In this blog post, we’ll focus on a specific subset of NSL tools: attribute-based filtering on segments. Segments typically correspond to chains or molecular fragments, and filtering them based on their properties—like the number of residues or structural groups—can be extremely helpful for protein modeling or large molecule analysis.
💡 Use Case: Selecting Segments with Many Residues
If you’re analyzing a molecular complex and want to focus only on the large chains, there’s a built-in attribute just for that: numberOfResidues. In NSL, this attribute is used as segment.numberOfResidues or more concisely s.nr.
Examples:
s.nr > 100– Matches all segments with more than 100 residues.s.nr 100:130– Matches segments with between 100 and 130 residues.
This is useful for scripting selections, preparing systems for simulation, or even just organizing views in complex molecular models.
🔍 Filtering by Number of Structural Groups
Another attribute is numberOfStructuralGroups (short: s.nsg), which gives you an idea of how chemically diverse or modular a segment is.
Examples:
s.nsg > 10– Filters for segments with more than 10 structural groups.s.nsg 10:12– For segments with a structural group count between 10 and 12.
🤔 Why is this useful? Structural groups include functional chemical fragments or individual residues in coarse-grained representations, so filtering by nsg can isolate segments that are more functionally significant or chemically interesting.
📌 Pro Tips
- When performing batch selections, combine filters. E.g.,
s.nr > 120 and s.nsg > 10. - Use this functionality in the Node Specification Editor to build reusable selection templates.
- Rapid filtering = faster workflows, especially when navigating large structural models.
You don’t have to click through the structure multiple times or write external scripts to isolate segments. Using s.nr and s.nsg directly in SAMSON leverages the NSL engine for efficient internal filtering.
For a full list of segment attributes and usage examples, visit the NSL segment documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.