When exploring or refining large biomolecular systems, molecular modelers often face the frustrating challenge of navigating through numerous chains trying to isolate just the ones relevant to their study. Whether you’re interested only in chains with a high number of residues, a specific number of segments, or particular formal charges, manually identifying them can be time-consuming, slowing down modeling workflows.
The Node Specification Language (NSL) in SAMSON offers a clean solution to this pain point by allowing users to filter chains based on their attributes using short, human-readable commands. Here, we’ll explore the chain attribute space in NSL, specifically focusing on chain-specific attributes to help you streamline your modeling process.
Why Filter Chains?
Let’s say you’re analyzing a protein complex with dozens of chains, but your interest lies in examining chains with more than 130 residues, or chains that have between 2 and 4 segments. Instead of clicking through tree nodes or sifting through thousands of atoms, NSL allows you to filter the view programmatically and interactively with queries like:
c.nr > 130– to find chains with more than 130 residuesc.ns 2:4– to find chains with 2 to 4 segmentsc.nsg > 10– to identify chains with a rich set of structural groups
Core Chain Attributes for Filtering
These chain-specific attributes support powerful query combinations:
| Attribute | Short Name | Usage Example |
|---|---|---|
| chainID | id |
c.id 2:4,6 – select chains 2 to 4 and 6 |
| numberOfResidues | nr |
c.nr > 130 – chains with large residue counts |
| numberOfSegments | ns |
c.ns < 3 – fewer segment chains |
| numberOfStructuralGroups | nsg |
c.nsg 10:13 – moderate grouping density |
NSL also allows more advanced operations such as combining filters and negating results:
c.nr > 130 and not c.h– residues-heavy and not hiddenc.id 1,3 and c.nr 100:200– chains 1 or 3 with medium residue counts
Interactive Browsing with NSL
Once filters are applied in SAMSON’s Desktop interface using NSL expressions in the filter bar or Selection editors, chains that meet the criteria become immediately highlighted. This can significantly reduce time spent scanning models and enable rapid iteration during design or analysis. For example, examining folding patterns only in large chains or comparing structural units among chains with 3 segments is only seconds away.
How It Adds Up
If you’re dealing with large PDB files or working on protein-protein interaction systems, the ability to search and isolate chains by clear attribute-based logic can save minutes or even hours in a modeling session. Over weeks or months, that adds up significantly across projects.
NSL brings back control to the user – making your workspace cleaner, your logic more reproducible, and your modeling sessions more focused.
To learn more about how to use chain attributes in NSL queries, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.