When working with complex molecular systems, it’s not unusual to feel overwhelmed by the sheer amount of structural data at your fingertips. Whether you’re preparing a model for visualization, simulation, or export, quickly narrowing down to specific features can save time and reduce errors.
One of the persistent challenges for molecular modelers is efficiently selecting side chains that match specific chemical and structural criteria. This could be side chains that have a high number of hydrogens, a particular formal charge, or contain certain types of atoms. If you’re using SAMSON, the powerful integrative platform for molecular design, you’re in luck: the Node Specification Language (NSL) makes this process much easier.
In this post, we’ll focus on a way to filter side chains based on their composition using NSL’s capabilities. The goal is to help you retrieve exactly what you need within large biomolecular structures using clear, declarative queries.
Why Would You Want to Filter Side Chains by Composition?
- You want to highlight side chains based on how many atoms they contain.
- You need to find charged residues to investigate electrostatics.
- You want to identify hydrophobic or hydrophilic side chains based on the number of carbon or oxygen atoms.
- You are preparing a selection for further simulation or visualization purposes.
How NSL Helps You Take Control
In SAMSON, side chain attributes can be accessed using the sideChain attribute space, shortened as sc. For example, if you want to filter side chains with 10 to 20 carbon atoms, use:
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sc.nC 10:20 |
Here’s a breakdown of several useful filters you might want to try:
- Number of atoms:
sc.nat
Filter side chains containing fewer than 100 atoms:sc.nat < 100 - Number of hydrogens:
sc.nH
Focus on hydrogen-heavy side chains:sc.nH > 15 - Formal charge:
sc.fc
Isolate positively charged side chains:sc.fc > 0 - Partial charge:
sc.pc
Search for strongly polarized residues:sc.pc 1.5:2.0
You can also combine conditions for more targeted queries. For instance, to find side chains that are both positively charged and contain more than 5 nitrogen atoms:
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sc.fc > 0 and sc.nN > 5 |
How This Saves You Time
Instead of manually inspecting side chains or scripting complex selection workflows, you can use concise NSL expressions in SAMSON’s search interface. This significantly reduces the time needed to prepare input data for visualization or simulation, especially when working with large protein or nucleic acid structures.
Here’s a quick example to inspire your workflow: suppose you are modeling interactions between small molecules and amino acid residues. You might want to compare side chains with high electronegativity. With NSL, that’s as simple as:
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sc.nO > 2 |
This retrieves side chains containing more than two oxygen atoms — often a signal of polar or charged functional groups.
Learn More
This is just the tip of the iceberg of what NSL can do with side chains. For a full list of side chain attributes and examples, explore the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.