When working with biomolecular models, it’s common to deal with multi-chain systems, including proteins with several subunits or complexes with ligands. But what if you’re trying to pinpoint just the monomeric structures? Or maybe you’re only interested in dimers or trimers? Navigating large datasets becomes repetitive if you can’t filter molecules based on the number of chains they contain.
Fortunately, SAMSON’s Node Specification Language (NSL) makes this easier by providing built-in molecule attributes that help you narrow down your selections efficiently—and programmatically.
Why Chain Count Matters
The numberOfChains attribute is particularly useful when handling large structures or screening molecule collections. Instead of manually inspecting each molecular node, you can specify precise selection criteria using the NSL. This saves time when preparing your systems for structural analysis, simulations, or visualization.
Meet molecule.numberOfChains (mol.nc)
The molecule.numberOfChains attribute (short name: mol.nc) is used to identify molecules that contain a specific number of chains. It accepts integer values and supports both inequalities and ranges.
Examples:
mol.nc < 3— selects molecules that have fewer than 3 chains (e.g., monomers or dimers)mol.nc 2:4— selects molecules that have 2, 3, or 4 chains (e.g., dimers, trimers, tetramers)
These simple expressions can be used in selection filters throughout SAMSON: in scripts, advanced selection dialogs, or visual queries.
Real-World Scenarios
Let’s say you have imported a large biological assembly from the PDB, and now you want to isolate all its monomeric units for independent simulations. Instead of clicking through the Document Explorer, just use:
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mol.nc 1 |
This will highlight all molecules containing exactly one chain.
Working on protein-protein interactions and want only dimers and trimers?
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mol.nc 2:3 |
Use this expression before exporting to simulation tools to reduce the system size or focus on specific complex arrangements.
Bonus: Combine with Other Attributes
You can make even more refined selections by combining mol.nc with other attributes. For example, molecules with two chains and at least 100 residues:
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mol.nc 2 and mol.nr > 100 |
This is especially useful in high-throughput environments or when working with automated preprocessing pipelines.
The numberOfChains attribute is a small but powerful feature that helps streamline workflows and improve selection accuracy in SAMSON.
To learn more and explore all available molecule attributes in NSL, visit the documentation page:
https://documentation.samson-connect.net/users/latest/nsl/molecule/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.