Quickly Filter Conformations by Atom Count in SAMSON

When working with complex molecular systems in SAMSON, molecular modelers often deal with large sets of conformations. These may include snapshots from simulations, different poses from docking, or generated conformational ensembles. However, identifying conformations that meet specific structural criteria—like having a certain number of atoms—can quickly become tedious without the right tools.

Fortunately, SAMSON’s Node Specification Language (NSL) supports advanced queries through attribute spaces, making it easy to filter conformations with precision. In this post, we’ll focus on how to use the conformation.numberOfAtoms attribute—also known as co.nat—to quickly find the conformations that matter most for your analysis.

Why Filter by Atom Count?

There are many situations where this is useful:

You want to isolate conformations of ligands or small molecules based on size
You need to exclude incomplete conformations, e.g., generated by a faulty script or damaged file
You’re doing metrics-based filtering to compare atom count variations among decoys or docked poses

Matching Conformations with NSL

To filter conformations by atom count, use the co.nat attribute. Here are two powerful ways to use it:

1. Find conformations larger than a specific size

For example, to find all conformations that contain more than 100 atoms:

co.nat &gt; 100

1	co.nat > 100

2. Select conformations within a range of atom counts

This is particularly helpful when working with conformers of similar size, for consistency in analysis:

co.nat 100:200

1	co.nat 100:200

This command matches all conformations that have between 100 and 200 atoms.

Combine with Other Attributes

You can also combine this filter with others to narrow your scope. For instance, this query filters selected conformations with more than 150 atoms:

co.selected and co.nat &gt; 150

1	co.selected and co.nat > 150

Use Case Example

Let’s say you’ve imported hundreds of conformations into SAMSON after running a conformer generation task for a molecule with flexible side chains. You notice some conformations have fewer atoms because of partial generation or artifacts. Instead of manually browsing through them, just select what you need with:

co.nat &gt; 95

1	co.nat > 95

This way, you’re immediately focusing only on the successfully generated structures. Less scrolling, more science.

Best Practices

Always double-check atom counts when filters return zero results—there may have been an issue with data loading
Use co.n or co.selected in combination to further refine your studies
Save your NSL queries if you often repeat similar filtering operations

For a complete list of attributes available in the conformation attribute space, visit the official documentation page linked below.

Learn more here: https://documentation.samson-connect.net/users/latest/nsl/conformation/

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