Quickly Find Segments with Specific Molecular Properties in SAMSON

When designing or analyzing biological macromolecules, one of the most time-consuming tasks is filtering or locating specific parts of your molecular model. For example, you might need to:

• Find all protein segments with more than 100 residues
• Identify RNA segments with an unusual number of structural groups
• Distinguish between segments based on their atomic or compositional properties

Doing this manually can feel like searching for a needle in a haystack—especially in large models. This is where the Node Specification Language (NSL) in SAMSON becomes especially useful.

Segment-Level Attributes: Precision Filtering 📍

SAMSON provides a compact and expressive way to filter segment nodes using their attributes. These attributes include both general node properties and segment-specific properties such as number of residues or structural groups. They can be referenced using short names, making queries quick and readable.

Examples You Can Use Right Away

Let’s say you want to select all segments with more than 130 residues. The query is:

Or, you might want to find segments whose number of residues lies between 100 and 130:

This kind of search can quickly help isolate long protein chains or identify potential modeling issues.

Filter by Number of Structural Groups

You can also query segments based on how structurally subdivided they are. For example:

This matches segments with more than 10 structural groups. Or for tighter control:

Combining Query Attributes

The real power of the Node Specification Language lies in combining different criteria:

With this, you’re only selecting segments that are both long and structurally subdivided. These may be protein domains of interest or segments worth further inspection or analysis.

Why This Matters

Molecular modelers typically manage complex systems with thousands of atoms or more. The ability to zoom in on parts of the system based on abstract molecular attributes saves time and ensures analytical precision. Whether you’re modeling protein folding, drug docking, or simulating conformational changes, filtering segment nodes with NSL improves efficiency.

These filters can be particularly helpful when used in conjunction with SAMSON’s visual and editing tools. For example, immediately selecting all segments with high residue count can help in adjusting representations, analyzing charges or preparing simulations.

To explore the full list of attributes that can be queried at the segment level, including numberOfAtoms, formalCharge, or partialCharge, consult the full documentation page below.

Read more in the official documentation.

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