If you’re modeling biomolecular systems, navigating large molecules to find specific side chains with certain characteristics can be time-consuming. Whether you’re optimizing a binding site, running electrostatics calculations, or preparing a molecule for coarse-grained simulations, filtering side chains by their properties can save valuable time.
In this post, we’re looking at how SAMSON’s Node Specification Language (NSL) allows you to filter and select side chains using a wide variety of attributes — all accessible through simple, readable queries.
Why Side Chain Filtering Matters
Side chains define the unique chemistry of amino acids. Identifying those with specific charges, element composition, or naming patterns is essential for tasks ranging from mutagenesis planning to computational docking. Instead of manually inspecting each residue, what if you could instantly highlight all positively charged side chains, or those with a high number of carbon atoms?
In SAMSON, this becomes straightforward using the sideChain attribute space (or sc for short). This attribute space gives access to side-chain-specific properties and lets you build flexible queries for visualization or scripting.
Getting Started: Querying Side Chains
Here are some simple examples:
- Find side chains with formal charge greater than zero:
sc.fc > 0 - Find side chains named “LYS” or similar:
sc.n "LYS"sc.n "LY*"(wildcards supported) - Locate side chains with >10 carbon atoms:
sc.nC > 10 - Filter by partial charge range:
sc.pc 1.5:3.0 - Select hidden side chains:
sc.h - Find side chains with visibility flag disabled:
not sc.vf
Understanding Key Attributes
The side chain attribute space inherits from two other spaces — node and structuralGroup — giving you access to multiple filters:
numberOfAtoms(nat): total atoms in the side chainnumberOfCarbons(nC),numberOfHydrogens(nH),numberOfNitrogens(nN), etc.: element-specific filtersformalCharge(fc): total formal chargepartialCharge(pc): total partial chargename(n): name pattern
How This Saves You Time
Instead of manually selecting and checking side chains one by one in a large structure, a single line of NSL can return precisely what matters to your simulation setup or hypothesis. Filter, highlight, or even automate processing steps depending on the chemical composition of your model.
Want to hide all side chains that don’t have material assigned? Try:
not sc.hm
Need to highlight all visible, selected residues within a certain charge range?
sc.selected and sc.v and sc.fc -2:2
Combining Filters
NSL supports logical operators, so you can chain multiple attributes:
|
1 |
sc.n "ARG" and sc.fc > 0 and sc.nC > 5 |
This returns Arginine side chains with positive charge and more than five carbon atoms — useful, for example, when analyzing active sites or conducting mutagenesis scans.
One More Tip: Coarse-Grained Models
Working at a higher level of abstraction? Use sc.ncga to select side chains based on their number of coarse-grained atoms:
sc.ncga < 50
This is essential when preparing models for coarse-grained MD simulations or analyzing simplified structures.
Conclusion
Using the side chain attribute space in SAMSON’s NSL provides an efficient, readable way to perform advanced selections based on structural or visual properties. It adds an important layer of control for molecular modelers working on complex systems.
To learn more about every attribute and how it’s inherited, visit the complete side chain attribute documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.