When working with macromolecular structures, a common challenge for molecular modelers is to efficiently identify and manipulate residues that meet specific biochemical or structural criteria. Whether you’re preparing a protein for simulation, adjusting protonation states, or studying interactions near active sites, selecting the right residues is crucial.
SAMSON’s Node Specification Language (NSL) provides a powerful and compact way to do just that. In this post, we’ll explore how to use NSL to select residues based on their charge, polarity, or structural properties—directly addressing a key pain point for molecular modelers.
🔍 Selecting Charged Residues
Need to identify all negatively charged amino acids in a protein? In NSL, this can be done quickly:
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r.c neg |
This matches residues with a negatively charged side chain.
You can also select multiple charge states at once, for example to highlight both neutral and positively charged residues:
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r.c neu, pos |
This flexibility allows you to isolate groups of interest for visualization or further analysis.
⚛️ Filter by Polarity
To locate residues based on side chain polarity—acidic, basic, polar or nonpolar—you can use:
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r.p acidic |
This will match acidic polar amino acids like ASP or GLU. You can combine polarity groups too:
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r.p basic, polar |
Perfect for selecting residues that may participate in hydrogen bonding or salt bridge formation.
🧬 Select Secondary Structure Types
Want to isolate residues in alpha helices or beta strands? Use the secondary structure attribute:
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r.ss h</code> <!-- helix --> r.ss a, b</code> <!-- alpha or beta --> |
This can be especially useful when analyzing folding patterns or protein domains.
🔢 Work with Residue Numbers
Precise control is possible via residue sequence numbers. For example, select residues 10 to 30 and 50 to 60:
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r.id 10:30, 50:60 |
Great for selecting domains, loops, or binding sites defined by residue indices.
🌐 Combined Queries
One of NSL’s strengths is that you can combine multiple conditions. For instance, find all acidic polar residues in alpha helices:
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r.p acidic and r.ss a |
This level of granularity helps streamline selections that would otherwise require extensive manual inspection.
Why This Matters
Modelers often spend significant time crafting selections manually. With just a few typed expressions, NSL empowers users to define highly specific residue subsets, such as:
- All neutral polar residues in a loop
- Terminal residues involved in salt bridges
- D-amino acids with high pKa values
This can drastically reduce time spent preparing systems for MD simulations, docking, or structural analysis.
To explore the full range of residue attributes available in NSL, including name, type, backbone completeness, and more, visit the official documentation:
https://documentation.samson-connect.net/users/latest/nsl/residue/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.