Quickly Isolate Segments by Atom Counts in SAMSON

When dealing with large biomolecular systems, one of the frequent frustrations for molecular modelers is filtering and navigating through complex segment structures — especially when each segment may have hundreds or thousands of atoms. How do you swiftly locate the segments you care about, such as those with a specific number of atoms, carbons, hydrogens, or even partial charge values?

If you’re using SAMSON, the integrative molecular design platform, there’s a built-in solution: filtering segments using their attributes through the Node Specification Language (NSL). This mechanism lets you write concise queries that find exactly what you need, without sluggish manual selection or scripting. 🧬

Segment-Level Filtering Made Easy with NSL

The segment attribute space in NSL (short name: s) targets segments with rich property definitions. By combining inherited attributes from structuralGroup, modelers can use NSL to quickly identify segments based on underlying atomic composition or electrostatic characteristics.

Filter by Atom Count

To locate segments with fewer than 100 atoms:

Or, to select those between 100 and 200 atoms:

Filter by Specific Atom Types

Need to examine segments rich in carbon? Use:

Or hydrogen-rich segments:

Filters are available for nitrogen (s.nN), oxygen (s.nO), and sulfur (s.nS) as well.

Use Partial Charge Filters to Locate Functional Segments

Sometimes you’re looking for highly charged regions. Try:

This targets segments with partial charges above 1.5. You can narrow the range too, for example:

Why Use NSL Instead of Manual Selection?

• Speed: Avoid browsing hierarchies or manually inspecting segments.
• Reproducibility: Save and reuse your queries instead of repeating GUI steps.
• Precision: Apply numeric or boolean filters with exact ranges.

Combining Filters

NSL also allows compound queries. For example:

This returns segments with fewer than 150 atoms, but more than 30 hydrogens.

When to Use It

This is especially useful when:

• Exploring coarse-grained models to focus on relevant regions only.
• Identifying chemically rich or structurally dense regions.
• Preparing systems for analysis, filtering by formal charges.

Explore these segment-level attributes and get more control over your molecular systems quickly and accurately, without distraction or extra coding.

To learn more, visit the official documentation page here: https://documentation.samson-connect.net/users/latest/nsl/segment/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.