When working with molecular models, positioning atoms and molecules precisely is essential. Whether you’re setting up a molecular fragment for docking or preparing a scene for visualization, having full control over the position and orientation of components can save hours of frustration. This is where Move Editors in SAMSON come into play.
If you’ve ever tried to adjust a molecule’s pose manually, you know how tedious and imprecise it can get. SAMSON makes positioning much smoother and more intuitive with three specialized tools: Displacer, Local Move Editor, and Global Move Editor. Each is tailored for specific movement styles, helping users to translate and rotate objects with precision. Let’s focus on the Local Move Editor, a favorite for manipulating molecular fragments in the molecule’s own frame of reference.
What Is the Local Move Editor?
The Local Move Editor lets you translate or rotate selected atoms or molecules along their principal axes. This is particularly useful when you’re manipulating individual fragments while preserving their local orientation. Compared to moving in the global XYZ frame, working in the object’s local frame can be more intuitive – especially for rotating side chains or aligning domains.
You can activate the Local Move Editor in SAMSON by pressing M, or selecting it from the left menu in the viewport. Once active, select the atoms or objects you want to manipulate. If you’re using the rectangle selection editor, it’s easy to grab exactly the group you need.
Tools Within the Editor
- Central translation widget: Move objects in the plane of the screen (camera plane).
- Side translation widgets: Move along principal local axes (X, Y, Z).
- Side rotation widgets: Rotate around local axes using curved arrows.
- Trackball: Freely rotate the object in 3D using the sphere widget.
Widgets are color-coded to correspond to the axes (light blue for X, mid blue for Y, dark blue for Z), which helps visualize the direction of transformation you’re applying.
Snapping and Precision
Need more control? You can enable snapping so that translations or rotations occur in fixed increments. For example, translating in steps of 0.5Å or rotating by 10°. This is especially helpful when aligning repeating structures or setting precise poses for analysis. Snapping preferences are accessible in the top-left menu of the viewport or via Interface > Preferences > Editors > Snapping.
Tweaking Parameters
Want exact angles or distances? You can right-click on the widgets or Ctrl/Cmd + click to manually enter exact values for translation or rotation. This brings in an additional level of control useful when setting up symmetric configurations or testing conformational spaces.
A Quick Workflow
- Load a molecule or import an asset.
- Select part of the structure (e.g., a side chain or ligand).
- Activate the Local Move Editor (
M). - Use the central widget to translate in the view plane, or side widgets for local axis-specific moves.
- Rotate with curved arrows or the trackball, with or without snapping.
- Right-click or use modifier keys to enter values manually.
Why It Matters
Being able to move parts of a molecule precisely is not just about aesthetics. Aligning fragments is critical for setting up simulations, modeling interactions, or analyzing internal degrees of freedom like torsion angles. The Local Move Editor offers exactly the right degree of freedom and flexibility for these tasks, without switching to code or using external tools.
Want to explore deeper? Head over to the full SAMSON documentation on moving objects.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.