When working with large molecular systems, it can be challenging to isolate meaningful parts of a structure, especially when dealing with complex proteins or multi-component assemblies. Molecular modelers often need to find and inspect specific segments—such as those containing many residues—which may correspond to entire protein chains, RNA sequences, or large molecular domains. But manually selecting these segments can be tedious and error-prone, particularly in big systems.
This is where SAMSON’s Node Specification Language (NSL) becomes particularly helpful.
Segment Attribute: numberOfResidues
In NSL, segment nodes can be filtered using the numberOfResidues attribute (short name: s.nr), allowing you to target segments based on how many residues they contain. This is especially useful for quickly focusing on larger molecular features or filtering out noise in massive simulation files.
Let’s look at two typical use cases:
s.nr > 100: This expression selects all segments that contain more than 100 residues. It is useful if you’re focusing on large polypeptide chains, for example.s.nr 100:130: This narrows down the selection to segments with between 100 and 130 residues, letting you focus on mid-sized molecules or fragments with greater precision.
This way, you can efficiently isolate biologically relevant segments in a structure with hundreds or thousands of components.
How It Helps in Practice
Let’s say you’re working on a molecular system containing a multi-chain protein with ligands, solvents, and other small molecules. You only want to visualize or analyze the primary protein chains, typically larger in residue count compared to other components. Instead of manually clicking through the structure tree, you can write a quick NSL query like:
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s.nr > 150 |
Just type this in SAMSON’s NSL-based selection field, and immediately, only the relevant segments will be highlighted. This saves time and minimizes manual error—especially important when preparing selections for simulations, mutations, or visualization.
You can also combine this with visibility or selection flags to further refine what you want to do with the selected segments:
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s.nr > 150 and s.vf |
This would select only visible segments with more than 150 residues.
Why This Matters
Filtering by residue count can make a real difference when working on:
- Analyzing complex or multi-domain proteins
- Inspecting large biological assemblies
- Cleaning up structures before export or simulation
Knowing how to write expressive NSL queries for segment attributes gives you faster control over what you see and manipulate. It helps reduce noise, simplify structure navigation, and focus your work on what really matters.
You can learn more in the full documentation here, which also covers other segment-specific attributes like number of structural groups and elemental counts.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net.