Aligning molecular structures may sound simple, but anyone working at the atomic level knows that precision matters—whether you’re comparing docking poses, preparing figures, or building assemblies. If you’ve ever wrestled with rotating, translating, and centering molecules manually, this post is for you.
In SAMSON, molecular alignment is not only visual—it’s controlled, repeatable, and precise. Here’s how you can take advantage of tools built into the platform to align your structures efficiently and accurately.
Why alignment matters
Whether you’re assembling larger molecular systems, comparing structural similarities, or setting up initial configurations for simulations, aligning structures is an essential operation. Misaligned molecules can lead to ambiguous visualizations and errors in computation. SAMSON offers a few easy-to-use tools that solve this issue directly in the viewport.
Using the context menu for alignment
To quickly align structures in SAMSON:
- Right-click on a structure, or click on your current selection in the Document view.
- In the context menu, go to Move selection.
- Choose how to align your structure using options like:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, YZ, or XZ plane
This is particularly useful when standardizing orientations across datasets or aligning a molecule to a specific reference frame.
Understand the reference frame
Alignment in SAMSON is done with respect to the global reference frame—a fixed XYZ coordinate system spanning the viewport. To help you visually, you can activate the grid in the bottom menu of the viewport interface. This displays the XY plane at Z = 0, ensuring that when you align something to this plane, you know exactly where it’s going.
Tip
You can switch on the grid in the bottom menu of the viewport to see the global reference frame’s XY plane at Z=0.
Batch alignment and distribution tools
For more complex tasks, such as arranging multiple structures, meshes, or lights, SAMSON provides commands under the Edit menu:
- Edit > Align: Aligns selected nodes along common planes or axes.
- Edit > Distribute: Evenly spaces a group of nodes between defined bounds.
You can also right-click on a compass widget to access alignment commands directly in 3D space—another intuitive way to interact with molecular models.
Final thoughts
Aligning molecular structures doesn’t need to be a time-consuming series of manual transformations. SAMSON offers a set of powerful, precise tools to help you align structures for visualization, simulation, or modeling—all with just a few clicks. Once you get the hang of the context menus, compass widget, and grid reference, you’ll find complex layouts much easier to manage.
Learn more on the official documentation page
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.