Imagine you’re preparing to simulate a protein in a new solvent environment. One of the first steps is deciding which residues might interact more strongly with the environment—perhaps charged residues for pH-sensitive behavior, or polar residues for solvent-accessible surface analysis. In SAMSON, the integrative molecular design platform, this kind of targeted selection can be done quickly with the Node Specification Language (NSL). This post walks you through how to identify amino acid residues based on their charge and polarity using a simple query syntax in NSL—no scripting needed.
Why It Matters
Whether you’re calculating electrostatics, studying binding pockets, or modifying surface residues, selecting residues by their properties is frequently needed. Yet many modelers still do this manually—clicking on one residue at a time or visually inspecting color-coded structures. SAMSON’s NSL offers a much faster and more systematic way to do it.
Selecting by Charge
To filter amino acid residues based on their side chain charge, NSL lets you use the residue.charge attribute (short name: r.c). Here are the most useful values:
negative(neg): acidic side chains (like ASP, GLU)neutral(neu): uncharged polar residues (like SER, THR)positive(pos): basic side chains (like LYS, ARG, HIS)
Examples:
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r.c neg |
Selects negatively charged residues.
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r.c neu, pos |
Selects neutral and positively charged residues.
Selecting by Polarity
To go one step further, you might want to select residues based on polarity, another attribute available in NSL: residue.polarity (short name: r.p).
Available values include:
acidicPolar(acidic)basicPolar(basic)nonpolarpolarundefined(un)
Examples:
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r.p polar |
Selects residues with polar side chains.
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r.p acidic, basic |
Selects residues with acidic or basic polarity.
Why Combine Both?
Combining charge and polarity attributes can help identify regions important for binding or interfacial interactions. For instance, to find acidic residues that are also polar:
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r.c neg and r.p acidic |
This is an excellent way to spot residues like ASP or GLU that often form salt bridges or participate in proton transfer.
Visualizing Selections
Selections created this way can be used directly in SAMSON to isolate parts of structures, apply visual styles, or export data. It’s also helpful when defining atom groups for analysis or simulations.
Using NSL is not just faster—it also makes your workflow reproducible and easier to document.
Learn more about the full set of attributes you can use to filter residues in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.