When working with complex molecular systems, it’s common to generate or import large numbers of conformations. As this collection grows, one recurring challenge for molecular modelers is efficiently identifying and filtering conformations based on specific properties—like selecting only those with a certain number of atoms. SAMSON’s Node Specification Language (NSL) provides a straightforward solution to this by offering customizable attribute-based filtering for various node types, including conformations.
This post introduces a specific NSL attribute called conformation.numberOfAtoms (or co.nat for short), and shows how it can be used to pinpoint conformations with a desired range or number of atoms in your model. Whether you need to remove unnecessarily small fragments or focus on heavy molecules, this method is time-saving and helps streamline your modeling process.
Why filter by atom count?
Atom count can be a reliable proxy to estimate the complexity or significance of a conformation. When importing or simulating molecular systems, you might end up with a mix of:
- Ligands with a few dozen atoms
- Protein chains with thousands of atoms
- Artifacts or garbage structures with a handful of atoms
Being able to focus exclusively on conformations above, below, or within a specific range helps you analyze only what truly matters in the context of your project.
Using co.nat in practice
The numberOfAtoms attribute in the NSL conformation space allows you to query nodes using intuitive filters. Here’s how:
1. Find conformations with more than 100 atoms
Use the following expression:
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co.nat > 100 |
This selects only conformations with strictly more than 100 atoms.
2. Filter conformations between 100 and 200 atoms
If you want conformations in a specific size range:
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co.nat 100:200 |
This includes all conformations with atom counts between 100 and 200, inclusive.
3. Combine with name filters
NSL allows combining conditions. For example, to select conformations starting with the letter “L” and with over 100 atoms:
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co.n "L*" and co.nat > 100 |
Visual overview
Here’s a summary of the relevant attribute from the official documentation:
Common use cases
- Filtering docking results to retain only large, likely meaningful structures
- Excluding water molecules or ions with low atom counts during structure refinement
- Verifying expected size ranges during batch conformer generation
These examples demonstrate how co.nat becomes a small but powerful tool in molecular design workflows.
To learn more about what you can do with conformation attributes, visit the original documentation page: NSL Conformation Attributes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.