Filtering Side Chains by Atom Count in SAMSON with NSL

In molecular modeling, especially in protein design and ligand optimization, analyzing and selecting specific parts of a molecule based on structural characteristics can save time and improve precision. One frequent task is identifying side chains with specific compositions, such as the number of hydrogen atoms or the overall atom count. If you’re working with complex molecular structures in SAMSON, this can be simplified using the Node Specification Language (NSL).

Why side chain filtering matters

Side chains often determine the behavior, reactivity, and binding properties of biomolecules. If you’re studying mutational effects in proteins or surfacing potential binding pockets, you may want to isolate side chains with a high number of carbons or a specific partial charge range. Rather than manually clicking through structures or writing lengthy scripts, NSL provides a structured and readable way to do this.

The basics of side chain filtering

Attributes of side chains in NSL are accessible through the sideChain attribute space, which uses the prefix sc. You can query side chains by:

Total number of atoms (sc.nat)
Number of hydrogens (sc.nH)
Number of carbons (sc.nC)
Number of oxygens, nitrogens, sulfurs
Partial charge (sc.pc)

For example, to select all side chains with fewer than 100 atoms:

sc.nat &lt; 100

1	sc.nat < 100

To find side chains containing between 10 and 20 hydrogen atoms:

sc.nH 10:20

1	sc.nH 10:20

These expressions can be combined with logical operators if needed. For instance, select side chains with more than 5 nitrogens and a partial charge between 1.0 and 2.0:

sc.nN &gt; 5 and sc.pc 1.0:2.0

1	sc.nN > 5 and sc.pc 1.0:2.0

Filtering by visibility and other utility flags

You’re not limited to compositional attributes. NSL also allows filtering based on display and search states, such as:

sc.v: visibility (true or false)
sc.hm: has material
sc.selected: currently selected

This means, for example, you can isolate visible side chains that have a formal charge greater than 1:

sc.v and sc.fc &gt; 1

1	sc.v and sc.fc > 1

Quick tips

Short names make queries concise: use nC for number of carbons, pc for partial charge, etc.
To target side chains only, always prefix with sc.
Use ranges with colon notation: sc.nat 50:100

These tips allow fast navigation through molecular structures and provide molecular designers with direct answers to structure-based questions.

Conclusion

Whether you’re doing structural analysis, binding site studies, or simply cleaning large molecular models, mastering NSL filters for side chains can streamline your workflow greatly. It’s not only faster—it offers consistency and reproducibility in structural queries to support high-quality modeling decisions.

To learn more, check the full documentation on Side Chain attributes in NSL.

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