Aligning molecular structures exactly as needed is a common task for anyone working in molecular modeling—whether you’re preparing a structure for simulations, visualizing interactions between different fragments, or simply making your model more visually interpretable. Many tools require scripting for such precision, but in SAMSON, you can perform structure alignment easily using built-in GUI tools—without writing a single line of code.
This blog post covers how to align molecular structures within SAMSON’s global reference frame. We’ll look at how to use the context menu and explore visual feedback for intuitive manipulation.
Why this matters 🧩
Incorrectly aligned atoms and molecules can introduce artifacts in simulation results and make interpretation harder. If a molecule is not centered or aligned along standard axes or planes, analyses and comparisons quickly become complex. Automating or scripting alignments can help, but sometimes users just want a fast and reliable manual approach—without switching to code.
Using the Document View Context Menu
You can align structures with respect to the global XYZ reference frame through SAMSON’s Document View. Here’s how:
- Right-click on your structure in the Document View or the 3D Viewport
- In the context menu, navigate to Move selection
- Choose a specific alignment option:
- Center on the origin
- Align with X / Y / Z axis
- Align with XY / XZ / YZ plane
This workflow allows you to center and orient structures consistently without ever leaving the GUI.
Visual Guide to Alignment
With just a few clicks, here’s what this looks like:
Each of these commands ensures you have atomic and molecular fragments oriented properly—critical for symmetry-aware analyses or visualization tasks.
Bonus Tip: Use the Grid
If you’re unsure where your selected structure is in the reference frame, turn on the grid using the bottom menu of the viewport. This grid shows the XY plane at Z = 0, giving you a visible reference for alignment.
No Need to Script
What makes this approach unique? There’s no scripting involved—it’s all built into SAMSON’s interface. For users who want reliable manual control (especially during early stages of modeling), this feature can save time and reduce errors.
When to Use This
- Before exporting data to simulation engines
- To visually compare conformations or fragments
- To construct complexes with properly aligned units
- To prepare videos or figures with clean orientation
Aligning structures precisely doesn’t need to be difficult. Whether you’re refining a model or preparing figures, this feature helps keep your work organized and reproducible.
To learn more, visit the official documentation page: 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.