Many molecular modelers often find themselves needing to align structures along specific axes or planes—whether it’s for preparing clean visuals, simplifying comparisons, or ensuring symmetrical arrangements for simulations. If you use SAMSON, you’ll be glad to know that aligning structures doesn’t have to involve tedious manual rotations or script commands. Built-in tools let you do this with a few right-clicks directly in the viewport.
This post will show you how to align molecular structures in the global reference frame in just seconds using SAMSON’s contextual menus and compass tool.
What is the global reference frame?
In SAMSON, the global reference frame consists of the standard XYZ axes and corresponding planes (XY, XZ, YZ). Aligning to this frame means positioning atoms or molecules according to global spatial coordinates—which is especially useful for editing, comparing, or building symmetrical molecular complexes.
Step-by-step: align molecules with a few clicks
1. Select the molecule or fragment
Use a selection method (like the rectangle selection editor) to select a structure in your scene.
2. Open the context menu
Right-click on the selected structure—or click on the selection in the Document view—to open the context menu.
3. Choose your alignment
Go to Move selection and pick how you want to align relative to the global axes:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, YZ, or XZ plane
Alternative method: align using the compass
SAMSON also features an intuitive compass widget. Right-click on the compass icon in the viewport to align your selection using similar options. This is a quick alternative if you’re working interactively and prefer a visual tool.
To assist with orientation, you can enable the grid in the bottom menu of the viewport. This overlays the global XY plane at Z=0, so you’ll have a visual reference during alignment.
When is this useful?
- Standardizing input for simulations
- Preparing comparative layouts
- Cleaning up structural models
- Building symmetric molecular assemblies
Whether you’re refining a ligand pose or arranging multiple biomolecules in a scene, precise alignment is just two clicks away.
If you’d like to go further, you can also use the Edit > Align and Edit > Distribute commands to control spacing between objects or use Python scripting for even more control.
To learn more about moving and aligning objects in SAMSON, visit the full documentation page here: 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.