When you’re modeling complex molecular systems, building everything from individual atoms can feel like reconstructing a cathedral with grains of sand. 🧱 For many molecular modelers, a common challenge is quickly and accurately building large or repetitive chemical structures—especially when the goal is to focus on functional behavior, simulations, or property analysis, not architecture 101.
Fortunately, SAMSON provides a streamlined way to assemble molecules using prebuilt molecular fragments (or “assets”). Whether you’re setting up biomolecules, polymers, functionalized materials, or nanoparticles, fragments can dramatically reduce the time and effort required. Here’s a close look at how to make the most of this feature, save clicks, and stay in the flow of science.
What Are Assets?
In SAMSON, assets are reusable molecular building blocks—functional groups, rings, radicals, small molecules, proteins, nanoparticles, etc. You can find them in the Asset Browser, which is populated with default libraries and can be expanded via SAMSON Connect.
The Asset Browser supports filtering and viewing options (grid/list view, image zoom) to help you find what you need quickly.
How to Use an Asset
Let’s consider you want to construct a simple organic molecule using phenol functional groups. Here’s how you’d do it in SAMSON:
- Go to the Aromatics folder in the Asset Browser.
- Double-click the phenol asset to load it into the Add editor.
- Click in the viewport to add a phenol molecule.
- Hover over existing atoms or bonds and click to connect new fragments through substitution or bonding.
SAMSON helps align and merge parts automatically, predicts fragment orientation, and gives visual overlays for valid/invalid substitutions (green is OK, red is not).
Build Your Own Fragments
You’re not limited to what’s in the default library—you can turn any selection into a reusable building block:
- Select a fragment in the viewport or Document view.
- Right-click and choose “Use selection to build”.
This adds your heterogeneous selection (custom sidechain, ligand, etc.) as a fragment ready for use in further assembly.
Tips to Go Faster
- Hold Ctrl (or Cmd on macOS) to select which atom or bond in the fragment becomes the connection point.
- Switch on interactive minimization (Z) while you build to automatically clean up bond distances and angles as you go.
- Use the Preferences panel to control automatic hydrogen adjustment, prevent implausible substitutions, and more.
And if you’re wondering—yes, you can move, rotate, and align fragments precisely. SAMSON has a range of editors and snapping tools for fragment positioning, which we’ll cover in a future post.
Why It Matters
If you’re building polymers, modeling ligands onto receptors, or preparing nano-constructs, fragment reuse gives structure to your workflow. It minimizes user error, drastically cuts editing time, and makes the platform friendlier to scripting and automation.
By including both a curated set of assets and the ability to make your own, SAMSON offers a flexible foundation for building molecular systems—one where you can focus your science efforts on simulations and insights, not assembly-line tedium.
Curious to explore all building features? Visit the official documentation page: Building molecules in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.