How to Select Negatively Charged Residues in Seconds

When working with biomolecular structures, identifying residues with specific properties—like charge—can be a recurring task. Whether you are focusing on the electrostatic interactions, preparing systems for simulation, or simply analyzing subsets of residues, quickly filtering negatively charged amino acids can save valuable time. Fortunately, SAMSON’s Node Specification Language (NSL) provides a powerful way to do just that through residue attributes.

Why charge matters 🧪

Charge is a key factor in molecular modeling. Negatively charged residues such as aspartate (ASP) and glutamate (GLU) often participate in salt bridges, bind metal ions, or occupy active sites. Efficiently filtering out such residues is crucial for tasks like:

Electrostatic surface visualization
Mutational analysis
Protein-ligand docking
Simulation setup

Instead of manually searching for the residue types every time, SAMSON’s NSL allows direct querying based on side chain charge.

Use `residue.charge` in NSL

SAMSON defines a residue.charge attribute, with a short name r.c, which directly captures side chain charge for amino acid residues:

neg or negative → negatively charged side chains
neu or neutral → neutral side chains
pos or positive → positively charged side chains

To find negatively charged residues, simply use:

r.c neg

r.c neg

This matches any amino acid residue with a negative side chain charge.

Make it even more specific

If you want to select atoms within negatively charged residues—for atom-based tasks or selections—just combine with a node type filter like this:

n.t a in r.c neg

1	n.t a in r.c neg

This matches atoms (n.t a) from residues (in r.c neg) that have negative side chain charges.

Combine with other properties

Need all negatively charged residues that are fully visible? Add another condition:

r.c neg and r.v

1	r.c neg and r.v

This fetches negatively charged residues that are also visible. You can keep extending the query, for example, fetching negatively charged residues in beta sheets:

r.c neg and r.ss beta

1	r.c neg and r.ss beta

Some practical examples

Here are a few use cases to get you started:

Highlight terminal, negatively charged residues: r.ter and r.c neg
Select backbone atoms of negatively charged residues: n.n "CA", "N", "C" in r.c neg
Turn material on/off for these residues only: Use selection with r.c neg, then apply material edits

Why this matters

Manually searching residue names or visually inspecting structures becomes increasingly inefficient as molecule size grows. By using residue.charge, you’re leveraging NSL not just for accuracy, but speed and reproducibility. These queries are also easy to script or reuse in larger workflows.

All these options and more are available in the SAMSON documentation. Check it out for additional attributes like polarity, hydrophobicity, pKa values, and beyond. SAMSON makes data-rich queries easily accessible without having to step out of your workflow.

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