When working with complex molecular systems, especially when comparing molecular structures, preparing input for simulations, or visualizing assemblies, it’s important to have your structures neatly positioned and consistently oriented. Yet too often, molecular modelers find themselves manually adjusting atoms and molecules, leading to inconsistent frames of reference and wasted time.
Fortunately, SAMSON simplifies the alignment task by providing built-in tools for aligning structures with the global reference XYZ frame. These features are often overlooked—even though they can make your workspace clearer and speed up your workflow significantly.
Why Align to a Global Frame?
Aligning molecular structures to a global frame is useful when you want to:
- Compare multiple structures side by side.
- Set up simulations with consistent starting positions.
- Design molecular assemblies where relative orientation matters.
- Ensure symmetry in spatial arrangements.
Without a consistent reference frame, interpreting results or combining molecules becomes frustrating and error-prone. SAMSON’s object alignment tools help solve this problem cleanly and quickly.
One-Click Alignment via Context Menu
To begin, simply right-click on a structure (such as a molecule, mesh, or light source) in the Document view, or click on the selected structure in the viewport. In the menu that appears, navigate to Move Selection. This brings up several options that let you:
- Center your object on the global origin
- Align with the X, Y, or Z axis (useful for orienting long molecules or vectors)
- Align with XY, XZ, or YZ planes (ideal for 2D arrangements)
For example, aligning a ligand with the Z-axis before docking it into a receptor can help ensure a more rational orientation and symmetry during calculations. The alignment commands are efficient and undoable, ensuring you can explore different setups without worry.
Make the Frame Visible
Not sure where Z=0 is? You can turn on the grid from the bottom menu in the viewport to see the XY plane. This helps you visually confirm alignment and improves control over positioning.
Tip: The grid only shows the XY plane at Z=0, but it still gives a reliable visual anchor.
Bonus: Compass-Based Alignment
If you prefer more interactive control, SAMSON also allows you to use the compass widget to align structures. Right-click on the compass to access alignment commands that correspond to major axes and planes.
Keep It Consistent
Whether you’re creating beautiful visualizations or scripting batch simulations, keeping your structures aligned can help maintain consistency across files, collaborators, and analysis pipelines. Best of all, these tools are accessible through a simple menu—no code required.
To learn more about aligning molecular structures in SAMSON, visit the original 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 https://www.samson-connect.net.