If you’ve ever found yourself painstakingly selecting amino acid side chains in a molecular model — trying to isolate features like high partial charge, large carbon content, or unusual visibility settings — you’re not alone. Manual selection becomes time-consuming and error-prone as the size of the molecular system grows.
The Node Specification Language (NSL) in SAMSON solves this issue by offering precise control over side-chain selection using readable queries. In this blog post, we’ll explore how the sideChain attribute space can streamline your workflow so you never have to dig through invisible atoms again.
Meet the sideChain Attribute Space
The sideChain attribute space (short name: sc) is designed specifically to work with side chain nodes. It provides access to both appearance-based info (like visibility or selection state) and structural/grouping data (like number of carbons or partial charge).
Visibility and Selection Attributes
Visual clutter is a common issue in molecular models. NSL lets you quickly identify hidden, visible, or selected side chains with straightforward expressions:
sc.h– selects hidden side chainsnot sc.v– selects side chains that are not visiblesc.selected– identifies the currently selected side chains
This is extremely useful for cleaning up a scene or debugging visibility problems when some atoms appear missing.
Structural Composition at a Glance
Let’s say you’re modeling ligand interactions and want to quickly locate charged amino acid side chains. Instead of manually checking residue by residue, one line does the trick:
sc.fc > 0 – finds positively charged side chains
Or if you’re focusing on hydrocarbon-rich environments in hydrophobic pockets:
sc.nC > 5 – selects side chains with more than five carbon atoms
Try narrowing down further with ranges:
sc.nH 10:20 – targets side chains containing 10 to 20 hydrogen atoms
This helps in residue classification and detecting chemically relevant subgroups faster.
Material and Ownership Flags
Material assignment is often used in visualization or simulation prep. Want to ensure that only side chains with custom materials are visible?
sc.hm and sc.om
This selects side chains that both have and own a material, meaning you’ve probably styled them purposely.
Why It Matters
Instead of zooming in and struggling through manual inspection, NSL string queries let you batch-select molecular features based on meaningful biological or chemical parameters. This streamlines visual analysis, scripting, or simulation preparation.
For example:
- Want to isolate buried residues? Try invisible ones:
not sc.v - Need polar side chains? Use partial charge:
sc.pc > 1.5 - Validate coarse-grained conversion? Filter by
sc.ncga
Whether you’re preparing molecular graphics or running a filtering script, mastering sideChain attribute queries can save hours of guesswork.
To browse the full list of attributes that can be used with sideChain, including short names and examples, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.