How to Query Side Chain Properties to Speed Up Molecular Selection

Molecular modeling often involves identifying very specific parts of a molecular structure: atoms with certain charges, residues with many hydrogens, or in the context of protein modeling, certain side chains with specific compositions or visibility states. Manually selecting these components can be time-consuming and error-prone.

Fortunately, if you’re using SAMSON, the integrative molecular design platform, there’s a streamlined way to query all sorts of structural features thanks to the Node Specification Language (NSL). One of its powerful capabilities is selecting side chains using a combination of Boolean and numerical filters. This post serves as a practical guide to side chain attribute queries to help molecular modelers accelerate their workflow.

What are side chain attributes in NSL?

In SAMSON’s NSL, side chain-specific queries live in the sideChain attribute space, abbreviated as sc. This means that when you’re targeting side chains in your structure, you’ll typically be writing expressions that start with sc.

These side chains inherit a large set of attributes from other node types. These attributes can be grouped in two useful categories:

• Binary attributes — such as visibility, selection status, or material ownership.
• Quantitative attributes — such as the number of atoms, hydrogens, or partial charge within the side chain.

Let’s look at how to practically use them to answer common questions scientists may face.

1. Selecting Invisible or Hidden Side Chains

If you’ve loaded a large biomolecule and parts of it are not displaying correctly, you might want to know whether some side chains are simply hidden.

You can use:

to select side chains that are hidden, or:

to select those that are not currently visible.

2. Highlighting Side Chains with Extreme Partial Charges

Examining charged regions can be essential for studying molecular binding or reactivity. You might want to find all side chains whose partial charge exceeds a certain threshold:

You can also specify a range:

3. Selecting Side Chains Based on Atom Counts

Interested in filtering side chains based on size? The numberOfAtoms attribute helps:

Or to get the medium-sized ones:

Additional atom-type specific filters include:

• sc.nC — number of carbon atoms
• sc.nH — number of hydrogen atoms
• sc.nO — number of oxygen atoms
• sc.nN — number of nitrogen atoms
• sc.nS — number of sulfur atoms

4. Matching Side Chains by Name

To target specific side chains by their assigned name, you can use:

to select all side chains with names beginning with “L”. You can also specify exact names using quotes.

5. Material-Based Queries

If you’re interested in rendering or applying different materials to side chains, the NSL supports material-bound filters:

• sc.hm — has material bound
• sc.om — owns material

This is helpful when tracking which parts of a structure will render with specific effects.

6. Combining Conditions

You can combine any of the above into logical expressions. For instance, to find visible side chains with more than 10 carbon atoms and a charge between -1 and 1.5, you can write:

Wrapping up

Side chain queries in NSL are especially helpful for protein modelers dealing with structural analysis, visualization, or preparing data for export or further simulation. By combining numerical and Boolean filters with short, readable syntax, you can make sense of huge molecular datasets without manual inspection.

To explore the complete list of side chain attributes and their usage, visit the full documentation page here: 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.