When analyzing protein structures, molecular modelers frequently need to isolate specific regions like alpha helices or beta sheets. These are not just structural features — they often play specialized biological roles, from enzyme active sites to membrane-spanning domains. However, in large and complex molecular systems, precisely filtering residues by their secondary structure can be tedious without the right tools.
The Node Specification Language (NSL) in SAMSON provides a concise and powerful way to do this. With the secondaryStructure attribute (short name: r.ss), you can easily select residues like:
- Alpha helices (
alpha/a/helix/h) - Beta strands (
beta/b/strand/s) - Unstructured loops (
unstructured/u/loop/l)
Let’s look at how this works in practice.
Select residues in alpha helices
To highlight all residues that belong to alpha helices, simply use:
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r.ss h |
This matches residues annotated as being in a helical conformation. It’s useful for visualizing structural motifs or region-specific dynamics.
Match multiple secondary structures
Need to work with both helices and strands?
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r.ss a, b |
This command selects residues in either alpha helices or beta strands. It’s particularly helpful when analyzing the core folded regions of a protein.
Isolate residues in loops
Unstructured regions can be rich in functional or flexible sites. Use:
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r.ss u |
…to isolate loops (also accessible as l for loop).
Combine with other attributes
Secondary structure queries can be combined with other criteria. For example, to find positively charged residues in helices:
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r.ss h and r.c pos |
This matches residues with positive side chain charge that are part of a helix, which may help identify surface-exposed sites or DNA-binding regions.
Why it matters
Whether you’re preparing a region for site-directed mutagenesis, analyzing molecular dynamics, or building coarse-grained models, quickly identifying structural regions is key. The NSL in SAMSON lets you do this precisely with simple readable queries — no scripts required.
To explore more secondary structure queries and their combinations, visit the original documentation:
Secondary Structure Documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit https://www.samson-connect.net.