Making Sense of Side Chains in NSL: What You Can Do with Side Chain Attributes

When working with complex molecular systems, it’s easy to lose track of specific structural elements. One group that often requires more detailed attention is the side chains. Whether you’re filtering out noise, performing structure-based modeling, or setting up simulations, being able to precisely define and query side chain attributes helps streamline your molecular design process.

SAMSON’s Node Specification Language (NSL) includes a dedicated sideChain attribute space (short name: sc), allowing you to pinpoint and manipulate side chain nodes efficiently. Here’s how to make this function work for you.

🔍 What can you filter by?

One of the most common frustrations among molecular modelers is identifying a subset of side chains based on specific physical or visual properties. NSL enables fine-tuned control with the following built-in attributes:

Visibility: Use sc.v to find visible side chains or not sc.v for hidden ones.
Hydrogen content: Query hydrogen-rich fragments using sc.nH > 10 or limit to moderate ranges like sc.nH 10:20.
Material ownership: With sc.om, check if a side chain owns its appearance data. This is useful for differentiating between stylized components and default representations.
Partial and formal charges: Use sc.fc and sc.pc to explore electrostatic features of your model without extra post-processing.

These flags help you narrow down parts of the molecular structure—critical when dealing with proteins, macromolecular complexes, or coarse-grained systems. For example, if you’re only interested in side chains with a partial charge above 1.5, you’d use:

sc.pc &gt; 1.5

1	sc.pc > 1.5

More complex queries, like retrieving side chains that are hidden, detached from visualization materials, and carry a formal charge greater than 3, would look like this:

not sc.v and not sc.om and sc.fc &gt; 3

1	not sc.v and not sc.om and sc.fc > 3

💡 Use Case: Cleaning Visualization for Publication

Ever struggled to get clean visuals for figures? Use selection- and visibility-related attributes like sc.selected, sc.h (for hidden), and sc.vf (visibility flag) to set up precisely what’s shown in your final render without manual clicking. For example:

sc.selected and sc.vf false

1	sc.selected and sc.vf false

This selects all side chains currently selected but with the visibility flag off, giving you rapid control over display settings directly through query.

🧬 Quantitative Filters Matter

Many properties accept range queries, which help slice systems in useful ways. Want side chains with a moderate number of atoms? Try:

sc.nat 100:200

1	sc.nat 100:200

…or, filter by specific elements, like carbon (sc.nC), nitrogen (sc.nN), oxygen (sc.nO), and sulfur (sc.nS) — all priceless when preparing functional analyses or identifying potential docking regions.

📘 Where to Go from Here?

The power of the sideChain attribute space lies in how precisely you can combine visual and physical filters. Whether tidying up visuals or performing deeper structural segmentation, NSL gives you tools to do it—all script-free.

To learn more and explore the full list of supported side chain attributes, visit the official documentation: https://documentation.samson-connect.net/users/latest/nsl/sideChain/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.