How to Select Charged Residues in SAMSON Using NSL

As a molecular modeler, it is often essential to quickly identify specific types of amino acid residues based on their chemical properties. One common need is to filter residues by charge state—for example, isolating positively charged residues when analyzing protein-solvent interactions or looking at salt bridge formations.

If you use SAMSON, the integrative platform for molecular design, you’re in luck! SAMSON’s powerful Node Specification Language (NSL) allows you to do this with ease—no scripting or Python required.

Why Does This Matter?

Residue charge affects everything from protein folding and stability to binding affinity and enzymatic activity. In large systems or simulations, manually identifying negatively or positively charged residues is time-consuming. With NSL, this can be done in one line.

Using NSL for Charge-Based Selection

In NSL, you can use the residue.charge attribute (short name: r.c) to match residues based on side chain charge:

Value	Short name	Description
negative	neg	Matches amino acids with negatively charged side chains (e.g., ASP, GLU)
neutral	neu	Matches amino acids with neutral side chains
positive	pos	Matches amino acids with positively charged side chains (e.g., LYS, ARG)
undefined	un	Residues with undefined side chain charge

Examples You Can Use Right Now

• r.c neg — Matches all negatively charged residues like aspartate and glutamate
• r.c pos — Matches positively charged residues such as lysine and arginine
• r.c neu, pos — Matches both neutral and positive residues, excluding negatively charged ones

These filters can be used in complex queries too. For example:

This matches atoms that belong to negatively charged residues, useful when visualizing or modifying a subset of a system.

More Than Just Charge

While filtering by charge is helpful, SAMSON’s NSL also allows you to combine this with other residue attributes like r.aa for amino acids, r.ss for secondary structure, and r.p for polarity. That means more precise, tailored selections. For example:

This matches atoms in negatively charged residues that are part of an alpha helix.

Conclusion

If you’re working with proteins or complex biomolecular structures, NSL in SAMSON offers an efficient and user-friendly way to segment your system by residue charge. It’s ideal for setting up simulations, analysis, or simply understanding your molecular system better.

To learn more about available attributes and example queries, check the full documentation at https://documentation.samson-connect.net/users/latest/nsl/residue/

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