Understanding and analyzing secondary structures like alpha helices and beta sheets is a routine task in molecular modeling, especially when dealing with proteins. Whether you’re preparing for simulations, setting up structure-based design workflows, or just need to isolate parts of a protein for visual inspection, being able to quickly identify and select specific structural elements can save a lot of time.
In SAMSON, the Node Specification Language (NSL) provides a concise and flexible way to select elements of molecular models based on a wide range of attributes. One particularly helpful capability is selecting residues based on their secondary structure.
Selecting Residues by Secondary Structure
The residue.secondaryStructure attribute (short name: r.ss) allows you to match residues based on their secondary structure using simple, readable queries. You can specify whether to select alpha helices, beta sheets, or unstructured regions (loops).
Available Options
- Alpha helix:
alpha,a,helix,h - Beta strand:
beta,b,strand,s - Unstructured (loop):
unstructured,u,loop,l
Aliases make the syntax very flexible and easy to adapt to your needs.
Examples
If you’d like to select all residues that belong to alpha helices, use:
|
1 |
r.ss alpha |
Or simply:
|
1 |
r.ss h |
To select residues in beta sheets:
|
1 |
r.ss b |
And if you’re interested in both helices and sheets:
|
1 |
r.ss a, b |
This can be particularly useful for isolating all structured elements of a protein.
Why It Matters
Protein secondary structure provides crucial hints about function and dynamics. By filtering residues based on structure using NSL, you can:
- Visualize only the functional elements of interest (e.g., helical motors, beta-sheet interfaces)
- Extract specific regions for simulations (e.g., just helices for coarse-grained modeling)
- Improve clarity in presentations or collaborative projects by hiding unstructured regions
Combined with NSL’s other capabilities (e.g., selecting by residue type, charge, or sequence number), this becomes a very powerful toolset for molecular modeling workflows.
Tip
You can also use secondary structure queries in combination with other selection criteria. For example, to select only histidine residues in helices:
|
1 |
r.t HIS and r.ss h |
This allows very targeted selections, based on both structural and chemical properties.
Try It Yourself
If you’re using SAMSON and haven’t used NSL queries like this before, try running a few on your favorite protein structure. The flexibility and speed of NSL, especially when working with large or domain-rich proteins, can make secondary structure-based selections much more efficient than using manual selection.
To learn more and explore the available options, visit the documentation page:
https://documentation.samson-connect.net/users/latest/nsl/residue/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.