How to Quickly Filter Bonds by Length in Molecular Models

One of the common challenges in molecular modeling is quickly identifying, analyzing, and working with specific bonds based on their characteristics. Among these, bond length is a key parameter. Whether you are analyzing the geometry of your molecule, identifying unusual interactions, or verifying model consistency, being able to filter bonds by their length is extremely useful.

If you’re using the NSL (Node Specification Language) in SAMSON, there’s a simple and powerful way to do this using the bond.length attribute (short name: b.len).

Why you might need to filter bonds by length

Modelers often encounter the following scenarios:

  • You suspect angles or lengths are off due to simulation errors or input data.
  • You are examining hydrogen bonds or weak interactions that fall in a specific range.
  • You are preparing data for quantum calculations and only want to retain bonds under a certain threshold.

Whatever the reason, filtering bonds based on length gives you immediate visual feedback and helps you refine your model more efficiently.

Using b.len in practice

The b.len filter lets you select bonds by setting precise ranges using angstroms (A) or nanometers (nm). Here are a few examples of how you might use it:

  • b.len >= 1.5A – selects all bonds that are 1.5 Å or longer
  • b.len 1.2A:1.4A – selects all bonds that are between 1.2 Å and 1.4 Å
  • b.len 0.15nm:2.1nm – equivalent range expressed in nanometers

The unit is specified right in the query, so there’s no ambiguity. This flexibility means you can adapt quickly depending on the level of detail in your project or the system you’re modeling.

What makes this useful?

Using NSL queries like b.len directly filters model components based on scientifically relevant criteria. It’s faster and cleaner compared to inspecting bond lengths manually or switching through various visualization modes trying to find outliers.

As a bonus, filtering doesn’t modify your model — it just highlights what you’re interested in. This makes it safe to use during exploration and quickly reversible if needed.

Pro Tip

Combine b.len with other NSL filters like bond order (b.o) or type (b.t) for more refined searches. For example:

  • b.len > 1.2A AND b.t s – selects long single bonds

To learn more about bond attributes in NSL, including examples for custom types and bond orders, check out the full documentation here.

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

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