Easily Select Residues Based on Charge and Polarity in SAMSON

Working with complex biomolecular structures often requires isolating specific types of residues, such as those that are charged or hydrophobic. This task frequently arises in molecular modeling workflows—whether you’re designing mutations, analyzing ligand binding, or preparing systems for simulations.

In SAMSON, the Node Specification Language (NSL) offers a convenient way to filter residues with high precision. In this post, we’ll explore how to use NSL’s residue.charge and residue.polarity attributes to quickly find amino acid residues based on their physicochemical properties, without having to manually browse through long sequence lists or 3D structures.

Why This Matters

Imagine you are analyzing an ionic interaction in a protein. You suspect that the interaction involves negatively charged residues, but you’re looking at a protein chain composed of hundreds of residues. Manually identifying these isn’t just tedious — it’s prone to error.

With NSL, you can write a simple expression like r.c neg to instantly highlight all negatively charged residues. Similarly, if you’re interested in all polar residues, you can use r.p polar.

Filtering by Residue Charge

The residue.charge attribute (short name: r.c) matches residues based on the charge of their side chains. Possible values are:

negative (neg)
neutral (neu)
positive (pos)
undefined (un)

Examples:

r.c neg → selects residues with negative side chain charge
r.c neu, pos → selects all neutral and positively charged residues

Filtering by Polarity

The residue.polarity attribute (short name: r.p) helps discover residues based on the polarity of their side chains. Possible values include:

acidicPolar (acidic)
basicPolar (basic)
polar
nonpolar
undefined (un)

Examples:

r.p polar → highlights all residues with polar side chains
r.p acidic, basic → selects residues that are either acidic or basic

Combine Attributes for Powerful Filters

What makes NSL especially useful is that you can combine filters. For example, this expression selects all polar, negatively charged residues:

r.c neg and r.p polar

1	r.c neg and r.p polar

Want to work on nonpolar, neutral residues only?

r.c neu and r.p nonpolar

1	r.c neu and r.p nonpolar

And thanks to SAMSON’s immediate visual feedback, you can quickly assess if your selection matches your understanding of the structure, reducing modeling mistakes.

Bonus: Apply to Atom Selection

You can also use these filters within broader selections, like selecting only atoms belonging to polar residues:

n.t a in r.p polar

1	n.t a in r.p polar

This helps you go even deeper into editing and analysis tasks.

To learn more about residue attributes and NSL, visit the full documentation page: documentation.samson-connect.net/users/latest/nsl/residue/.

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