Working with complex biomolecular structures can quickly become challenging when you’re dealing with large systems: proteins with multiple chains, cofactors, solvents, and more. One frequent need among molecular modelers is the ability to quickly isolate relevant parts of a structure. Chains, in particular, can carry large sets of residues and segments that may or may not be relevant to your current study.
In SAMSON, filtering specific chains based on quantitative attributes like the number of residues (numberOfResidues, abbreviated c.nr) and number of segments (numberOfSegments, abbreviated c.ns) is straightforward using the Node Specification Language (NSL). Knowing how to leverage these attributes can help reduce noise in your workspace and improve performance when visualizing or analyzing molecular systems.
Why filter by number of residues or segments?
Here are a few real-world cases where this becomes useful:
- Identifying main protein chains: Most main chains have 100+ residues. Filtering by
c.nr > 100helps quickly isolate them, excluding smaller ligands or artifacts. - Avoiding solvent noise: Some water clusters or ions might appear as small chains. Setting a threshold like
c.nr < 10removes many unwanted entries. - Distinguishing between different structural domains: Chains with more segments (e.g.,
c.ns > 2) could indicate complex folded structures or junctions worth investigating separately.
How to use queries in practice
Thanks to NSL’s concise syntax, this is how you can execute some common filters within SAMSON:
c.nr > 130– matches all chains with more than 130 residues.c.nr 100:130– matches chains with residue counts between 100 and 130.c.ns < 3– selects chains composed of fewer than 3 segments.c.ns 1:3– chain segments in a controlled range, often useful to include both monomers and some multimeric forms.
When combined with NSL’s other filtering tools, like chain ID (c.id), visibility (c.v), or atom count (c.nat), you can isolate extremely specific sections of your model.
Visual example: checking chain sizes
While this documentation section does not provide an image, you can quickly visualize this in SAMSON by loading a protein (e.g., a PDB file), opening the NSL filter input, and typing c.nr > 100 to see only chains with enough size to be meaningful for structural modeling or docking preparation.
Getting more sophisticated
You can also combine filters to pinpoint exactly what you’re looking for. Examples:
c.nr > 100 and c.ns < 3– Chains with many residues but limited complexity in segmentationc.nr 80:120 and not c.h– Medium-sized chains that are not hidden
Understanding how to filter with chain attributes makes SAMSON a far more efficient workspace for modelers who deal with large biomolecular systems.
Want to dive deeper into these possibilities? You can learn more in the official SAMSON documentation on NSL chain attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.