If you’re working on complex biomolecular systems, there’s a good chance you’ve needed to focus on a specific subset of residues — perhaps only charged amino acids, those in beta sheets, or ones located at sequence termini. Filtering and selecting these subsets quickly becomes essential to efficient model building, visualization, and analysis.
Using SAMSON’s Node Specification Language (NSL), created to query and manipulate molecular structures with precision, this task is much more manageable than you might expect. In this post, we’ll explore how to identify meaningful categories of residues within your models using NSL attributes. Whether you’re building simulations, preparing inputs for downstream tools, or just getting familiar with your system, this guide will provide practical selectors you can use right away.
Match residues with charge, polarity, and side-chain characteristics ⚡🧲
Charge and polarity at physiological pH are fundamental properties that control molecular recognition, transport, and folding. With NSL, you can select charged and polar residues with simple expressions:
r.c neg: Negatively charged residues like ASP and GLUr.c pos: Positively charged residues like LYS and ARGr.p acidic: Acidic polar side chainsr.p basic: Basic polar side chainsr.p nonpolar: Hydrophobic residues, important in membrane or core environments
This saves precious time over manually identifying residues based on three-letter codes or locations. For example, to highlight all charged residues, regardless of sign:
r.c neg, pos
Identify secondary structure elements in selections 🧬
It’s often useful to isolate residues based on the secondary structures they form. NSL supports these distinctions:
r.ss h: Alpha helices (also available usingalphaorhelix)r.ss b: Beta strandsr.ss u: Loop or unstructured regions
Combined with residue IDs, this becomes even more specific. For instance, to select residues in positions 40–60 that form helices:
r.ss h and r.id 40:60
Quickly find terminal and non-standard residues
Terminal residues play key roles during protein interactions and modifications. Use:
r.ter: All terminal residuesnot r.srn: Residues with non-standard names — helpful for spotting modified residues
Filter by residue type and range 📌
Let’s say you want to isolate all LYS, ARG, and HIS residues (the most common positively charged amino acids):
r.t LYS, ARG, HIS
Or, target all residues between indices 100 and 200:
r.id 100:200
Designing smart selections for simulation subsets
Suppose you’re preparing a system for enhanced sampling simulations and want to freeze all residues that aren’t in polar loops. Try:
not (r.p polar and r.ss u)
This intuitive representation helps define simulation boundaries without manual lookup tables or residue-name matches.
Final thoughts
Node Specification Language makes it easy to translate scientific intuition into precise structural selection criteria. Whether you’re identifying sites for mutagenesis, visualizing binding interfaces, or selecting flexible regions for enhanced conformational sampling, mastering residue attribute filters will streamline your modeling operations significantly.
To explore the full list of available attributes and learn more about their usage, visit the official documentation page:
https://documentation.samson-connect.net/users/latest/nsl/residue/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.