One of the most common challenges in molecular modeling is quickly identifying specific side chains based on their chemical properties. Whether you’re performing structure refinement, dataset curation, or preparing inputs for simulations, being able to filter out side chains based on atom types (carbon, nitrogen, sulfur, etc.) or formal charge can save significant time and reduce errors.
SAMSON provides a dedicated attribute space for side chain entities called sideChain (or short name: sc) within the Node Specification Language (NSL), making this kind of filtering easy and flexible.
Why does this matter?
If you’re trying to track charged residues, search for chemically reactive groups, or curate structurally interesting motifs, knowing how to query based on attributes like atom count or partial charge is essential. For example, maybe you’re modeling enzyme pockets and need to identify side chains with more than 5 hydrogen atoms. Or maybe you want to focus your analysis on neutral residues only.
Practical Examples with NSL
Here are a few useful queries you can run in SAMSON using the sc attribute space:
- Find side chains with more than 5 nitrogen atoms:
sc.nN > 5 - Select side chains with 1 to 3 oxygen atoms:
sc.nO 1:3 - Identify side chains with no sulfur:
sc.nS 0 - Display side chains with a partial charge over 1.5:
sc.pc > 1.5 - Filter out side chains with fewer than 100 atoms:
sc.nat >= 100
Each of these attributes corresponds to logical properties inherited from the structuralGroup attribute space. The full list available includes:
sc.fc– formalCharge (integers)sc.nat– numberOfAtoms (integers)sc.nC– numberOfCarbons (integers)sc.nH– numberOfHydrogens (integers)sc.nN– numberOfNitrogens (integers)sc.nO– numberOfOxygens (integers)sc.nS– numberOfSulfurs (integers)sc.ncga– numberOfCoarseGrainedAtoms (integers)sc.pc– partialCharge (floats)
Tips for Effective Querying
You can combine multiple attribute filters using logical operators to refine your selection further. For example:
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1 |
sc.nN > 2 and sc.nO < 1 |
This would find side chains with more than two nitrogen atoms but fewer than one oxygen atom.
Patterns like these can be crucial when preparing target-specific datasets, engineering mutations, or visualizing biochemical features of interest.
To explore all available side chain attributes and learn how to use them in NSL, visit the official documentation page:
https://documentation.samson-connect.net/users/latest/nsl/sideChain/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download and install SAMSON here.