Eliminating guesswork: how to search by bond length in SAMSON

As a molecular modeler, you’ve probably faced the challenge of identifying parts of a molecule where bond lengths deviate from expected values. Whether you’re validating experimental data, optimizing geometries, or preparing a simulation, being able to quickly locate and filter bonds by length can save hours of manual inspection.

Fortunately, the Node Specification Language (NSL) in SAMSON offers a precise and efficient way to do just that. In this post, we’ll explore how to use the bond.length attribute, which allows you to find bonds based on length ranges and thresholds directly in the SAMSON interface.

Why bond length filtering matters 🧪

Bond lengths are an essential structural feature. Deviation from expected values can indicate:

• Misassigned atom types in automatic parametrizations
• Geometric strain in ring systems or large molecules
• Results of faulty optimizations or input geometries

Whether working with small organic compounds or large biomolecules, filtering by bond length is often the first step toward structural refinement or error diagnosis.

Using b.len to search by bond length

In SAMSON, the short name for the bond.length attribute is b.len. Here’s how to use it:

🔍 Find bonds longer than a certain threshold

To find all bonds longer than 1.5 angstroms:

This is especially useful if you want to inspect possibly elongated bonds that might indicate unusual bonding situations or strained geometries.

📏 Find bonds within a precise length range

Do you need all bonds between 1.2 and 1.4 angstroms? Use:

You can also specify nanometers:

This flexibility is helpful when using structures from different sources with different unit conventions.

Best practices for cleaner queries

• Always specify your units (A for angstroms, nm for nanometers).
• Use ranges to avoid overly restrictive filters—chemistry isn’t always binary!
• Combine length filters with other attributes like b.t (bond type) for more powerful queries.

Use case: Highlight unusually long single bonds

To find all single bonds longer than 1.7 Å:

This could help identify structurally unstable bonds or incorrect assignments in imported geometries.

Visual inspection and export

After applying your query in the Find window, SAMSON will highlight matching bonds directly in the molecular viewport, making visual inspection and further editing easier. You can then isolate, export, or modify these selections as needed for your workflow.

With just a few characters in a query, you can scan large structures for length anomalies and interactively refine your models faster than ever.

To dive deeper into bond attribute filtering, visit the full documentation page: Bond attributes in NSL.

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