When analyzing macromolecular structures, it’s common to focus on particular subsets of residues—like side chains with a certain number of atoms, or ones rich in specific elements. Whether you’re modeling the behavior of hydrophobic patches or analyzing charged environments, being able to target just the right side chains can save hours and avoid errors.
In SAMSON, the Node Specification Language (NSL) lets you do exactly this by offering intuitive access to side chain attributes. Let’s look at how you can efficiently filter and select side chains based on their atomic composition using a few key filters in NSL.
Understanding Side Chain Filters
Side chains in NSL are accessible through the sideChain attribute space—shortened as sc. You can use a variety of attributes to filter these, based on data such as atom counts, charges, and visibility.
For example, if you want to select side chains with fewer than 10 carbon atoms, the NSL query would look like:
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sc.nC < 10 |
Or, to narrow it down to side chains with between 100 and 200 atoms in total, you would write:
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sc.nat 100:200 |
Available Filters
Here’s a quick overview of the elemental filters and what they represent. All of them accept integer values for flexible range queries:
sc.nC: Number of carbon atomssc.nH: Number of hydrogen atomssc.nN: Number of nitrogen atomssc.nO: Number of oxygen atomssc.nS: Number of sulfur atomssc.nat: Total number of atomssc.ncga: Number of coarse-grained atoms
Each of these can be combined with logical operations for even more precision. For instance:
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sc.nC 5:10 and sc.nO > 2 |
This selects side chains with between 5 and 10 carbon atoms that also have more than 2 oxygen atoms.
Advanced Use: Partial and Formal Charges
If your interest is in electrostatics, you can filter side chains using formal charges with sc.fc or partial charges via sc.pc. These can help identify potentially reactive or structurally important regions.
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sc.fc > 1 |
Additionally, partial charge filters accept float values, allowing for subtle electrostatic analysis:
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sc.pc 1.5:2.0 |
This expression filters for side chains whose partial charge lies between 1.5 and 2.0.
When Is This Useful?
These tools are especially handy when preparing systems for molecular dynamics or docking simulations. Perhaps your simulation engine is sensitive to the presence of certain atoms, or you want to track down inconsistencies in atomic composition between residues. Having precise, scriptable access to these features can greatly reduce setup time.
They’re also highly relevant for educational and documentation purposes—for example, illustrating how ionizable or hydrophilic side chains are distributed in a structure.
Conclusion
Whether you’re analyzing mutants, visualizing hydrophobic cores, or preparing inputs for force-field assignment, the ability to select side chains based on atomic criteria can streamline your workflow. The NSL makes this process both powerful and approachable.
To learn more about these options and explore additional filters, visit the official SAMSON documentation on side chain attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.