Quickly Select Atoms by Geometry with NSL in SAMSON

When modeling molecules, filtering atoms by chemical properties or structural features is an everyday task. Yet, for many molecular modelers, selecting atoms by geometry—like tetrahedral or octahedral configuration—can still be a tedious, time-consuming process, especially when working with large systems. If you’ve ever spent too much time manually isolating atoms based on how they’re bonded in 3D space, this post is for you.

Enter SAMSON’s Node Specification Language (NSL), a powerful query language built into SAMSON that allows you to describe exactly what you want to select—down to the geometry of atoms. Whether you’re studying catalysis, molecular design, or reaction centers, NSL can simplify your workflow dramatically.

Why filtering by geometry matters

Geometry plays a crucial role in molecular behavior—from hybridization to reactivity and even hydrogen bonding patterns. For example:

• Finding all tetrahedral carbon atoms in a large protein can help identify potential reactive centers.
• Selecting atoms with trigonal planar geometry could help define planar moieties involved in conjugated systems.
• When evaluating metal complexes, knowing which atoms are in octahedral coordination is essential.

This kind of context isn’t captured just by knowing the element or the bond count.

How to select by geometry using NSL

With NSL in SAMSON, filtering atoms by geometry is straightforward. The geometry attribute belongs to the atom attribute space, with short name a.g.

For example, to select atoms with tetrahedral geometry:

To select atoms that are either linear or octahedral:

Or find atoms with more exotic geometries like square planar:

Here’s a list of commonly used geometry short names:

• l: linear
• b: bent
• tpl: trigonal planar
• tet: tetrahedral
• o: octahedral
• spl: square planar

And many others, including seesaw, tpy (trigonal pyramidal), and d (dodecahedral).

Need to get more specific? NSL allows for combining queries to make complex selections. Want tetrahedral carbon atoms only? Use:

Or filter atoms that are trigonal planar and have more than 2 bonded atoms:

One note of caution

Before using the geometry filter, make sure that geometry has been computed or assigned within SAMSON. NSL relies on available computed properties, so if geometry hasn’t been calculated, your filter may not return expected results.

Simplify your selection tasks

Instead of hunting through visual renderings or writing custom scripts, NSL gives you expressive power right at your fingertips. Whether it’s selecting all tet atoms in an active site, or analyzing structural deviations, NSL-based geometry filtering can significantly speed up your modeling work.

Want to explore more about atom geometry and the full list of options? You can check the full documentation here: https://documentation.samson-connect.net/users/latest/nsl/atom/

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