When loading molecular structures into SAMSON, you may find yourself dealing with scattered orientations or off-center models. This seemingly minor layout issue can become an obstacle when you want to build larger systems, compare multiple conformations, or prepare your scene for rendering. How can you bring order to your workspace quickly and consistently?
SAMSON’s global reference frame alignment tools offer a set of simple yet powerful features to realign and reposition structures with precision and ease. Whether you’re creating a figure, preparing data for simulation, or just trying to keep things tidy, these tools are accessible directly through the context menu.
Aligning in the Global Reference Frame
The global reference frame corresponds to the XYZ axes in SAMSON’s viewport. Aligning your structures to this frame ensures consistent positioning and makes transformations predictable when working with multiple objects.
Aligning is straightforward:
- Right-click on the object or selection you want to align.
- From the context menu, select Move selection.
- Choose how you want to position it (e.g., Center on the origin, Align with YZ plane, etc.).
You can find options to:
- Center objects on the origin.
- Align with the X, Y, or Z axes individually.
- Snap objects to the XY, YZ, or XZ planes.
This helps create symmetry, standardize layout, and prepare for subsequent transformations like duplication or rotational operations.
Tip: Use the Grid
To gain more spatial awareness while aligning, activate the grid in the viewport using the bottom menu toolbar. This makes the XY plane at Z=0 visible and helps you see the effect of alignment in real time.
Want to go further? You can combine alignment with snapping and move editors to build precise spatial arrangements. For example, you could align all fragments to the XY plane, then distribute them using evenly spaced intervals with snapping settings enabled. This is particularly useful when constructing crystal grids, protein-ligand aggregates, or layouts for visual communication.
A Simple Workflow for Structure Cleanup
If you often receive molecular files from different sources and want to normalize their orientations, try this quick routine:
- Load your model into SAMSON.
- Select the entire structure.
- Right-click inside the viewport > Move selection > Center on origin.
- Repeat to align with one or more global axes or planes.
- Switch on the grid (optional) to confirm placement on global planes.
This small step helps ensure you’ll work in a clean, repeatable environment — whether you’re running simulations, rendering scenes for publication, or scripting automated pipelines.
To dig deeper into all available options, including distributing multiple structures and working with the compass widget, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.