When working with molecular models, even small inconveniences in object positioning can slow down your workflow. Whether you’re preparing figures for publications, aligning structures for simulations, or simply organizing your workspace, having molecules scattered arbitrarily in 3D space can be a hassle. Fortunately, SAMSON offers fast, visual methods to align and center molecular structures using the global reference frame.
Why alignment matters
Properly aligned structures can speed up docking or simulation workflows, ensure consistency across datasets, and produce clearer visualizations. If you’ve ever manually dragged molecules into place, you’ll appreciate SAMSON’s one-click centering and orientation tools.
Accessing alignment tools in SAMSON
In SAMSON, you can align atomic structures with respect to the global XYZ axes and planes. To do this:
- Right-click on a structure in the Document view or on a selected molecule in the viewport.
- Navigate to Move selection in the context menu.
- Choose from several alignment actions:
- Center on the origin
- Align with X / Y / Z axis
- Align with XY / XZ / YZ plane
This makes it easy to center one or multiple selected nodes, such as molecular fragments or entire structures.
Pro tip: Use the grid
If you’re aligning objects to the XY plane, you can switch on the grid from the bottom menu of the viewport. This will display the XY plane at Z = 0, giving you visual feedback during alignment.
Tip
You can toggle the grid in the viewport’s bottom bar to see the global reference plane (XY at Z=0).
Going further: Compass-based alignment
Want to skip the menus? SAMSON also lets you align molecules using the compass widget. Right-click on it, and a menu appears with quick access for alignment operations. It’s especially useful when dealing with multiple molecules or when positioning matters precisely.
Video example
In the following video, you can see how structures can be easily aligned and distributed using SAMSON’s interface:
To learn more about how you can align and distribute your molecular models in SAMSON, including batch alignment and snapping options, visit the official documentation:
https://documentation.samson-connect.net/users/latest/moving-objects/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.