In many molecular modeling projects, researchers often need to isolate and analyze specific side chains in a protein or peptide—those that carry a particular charge, belong to certain residue types, or contain defined atomic compositions. Doing this manually can be tedious and error-prone, especially as molecular systems grow more complex. Luckily, SAMSON’s Node Specification Language (NSL) can help automate these searches with precision and speed.
This post focuses on side chain attributes in the NSL, specifically targeting users who want to query proteins based on detailed properties like the number of atoms, formal charges, or atomic composition.
Why Query Side Chains?
Imagine you’re setting up a simulation or conducting an analysis and need to:
- Select all side chains with a positive formal charge.
- Find side chains that are hidden or visible in a scene.
- Isolate residues with more than 10 carbon atoms.
NSL allows you to build such queries quickly, and SAMSON applies them instantly. The power and expressiveness of the NSL come in handy for such specific tasks.
Using the sideChain Attribute Space
To focus on side chains specifically, NSL offers a dedicated attribute space called sideChain, abbreviated as sc. This space supports a wide array of inherited attributes from more generic node types. Here’s a selection of what you can query directly:
sc.fc– formal charge (e.g.,sc.fc > 0)sc.nC– number of carbon atoms (e.g.,sc.nC 10:20)sc.pc– partial charge (e.g.,sc.pc > 1.5)sc.nH– number of hydrogen atomssc.hidden– whether it’s hidden (trueorfalse)sc.name– name with string matching (wildcards supported!)
For example, if you are searching for side chains starting with the letter “L” and having more than 10 carbon atoms, your query inside SAMSON could look like this:
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sc.n "L*" and sc.nC > 10 |
You can also combine attributes using logical operators (like and, or, and not) to build complex queries with ease.
Understanding Atomic Composition Filters
The ability to count the number of atoms of a certain type (C, H, N, O, S) in a side chain makes filtering very precise. Here are some useful filters:
sc.nN < 3– Side chains with fewer than 3 nitrogen atoms.sc.nO 1:2– Side chains containing 1 or 2 oxygen atoms.sc.nS 0– Side chains without any sulfur.
If you’re screening for hydrophobic residues, this kind of attribute filtering is extremely useful for a rational design of peptides or proteins.
Quick Tip 🌟
When you’re unsure of the property names or ranges, just refer back to SAMSON’s interactive documentation or hover over attribute names in the GUI filter bar (if you’re using an Extension with visual query support).
The NSL also supports filtering based on visual representation and status flags. For example:
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sc.visible |
This query returns all side chains that are currently visible in the workspace. Combined with other filters, it becomes a powerful visual and structural selection tool.
Final Thoughts
Querying side chains using NSL in SAMSON can significantly speed up exploratory workflows and prepare selections for simulations, analysis, or visualization. If you’re working with complex biological molecules, efficient selection techniques save time and reduce manual errors.
Learn more and explore the full list of supported attributes in the NSL side chain documentation here: https://documentation.samson-connect.net/users/latest/nsl/sideChain/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.