Precise control over molecular geometries is a core part of any modeling or simulation workflow. Whether you’re adjusting a ligand orientation, fine-tuning a molecular assembly, or preparing a structure for simulation, moving atoms and molecular fragments accurately is essential. This is where SAMSON’s Move Editors come into play.
In this post, we’ll explore the different ways SAMSON allows you to manipulate structural elements via its integrated Move Editors. These tools provide molecular modelers with intuitive and interactive ways to move, rotate, and align molecular fragments within the 3D viewport.
Why this matters
Manual repositioning of molecular fragments is often a bottleneck in structural modeling. Standard molecular editors may require repetitive commands or limited 2D interfaces. SAMSON addresses this by providing 3D edit tools with visual feedback, snapping capabilities, alignment options, and more—boosting productivity while reducing errors.
Meet SAMSON’s Move Editors
SAMSON comes with three main move editors:
- Displacer: A basic tool for translating objects within the plane of the screen.
- Local Move Editor: Enables rotations and translations along local axes derived from the selected structure. Shortcut: M
- Global Move Editor: Allows precise movement along the global XYZ axes. Shortcut: K
Each editor provides a set of interactive on-screen widgets for translation and rotation. For instance, the Local Move Editor offers principal axis translation, rotation, and even a trackball widget for free 3D rotation. This is especially useful when refining dihedral angles or adjusting fragment orientations interactively.
Snapping for Precision
All move editors feature optional snapping functionality. You can enable snapping via the viewport’s top-left quick access menu or in Preferences under Interface > Preferences > Editors > Snapping. This makes it easy to:
- Match symmetrical positions in a molecular assembly
- Ensure consistent bond lengths or angles
- Replicate structural motifs with minimal error
Using the Editors
Here’s an example workflow using the Local Move Editor:
- Select a group of atoms with the rectangle selection tool.
- Activate the Local Move Editor (shortcut: M).
- Drag the central widget to translate in the screen plane, or use axis widgets for directional control.
- Use the curved arrows for rotation or the trackball for freeform orientation.
- Enable snapping and specify the snap value for fine-tuned adjustments.
The movements are undoable (Edit > Undo), ensuring you can always revert if needed.
Alignment and Distribution
The move editors integrate well with SAMSON’s Align and Distribute tools under the Edit menu. Whether you want to line up molecular subunits or distribute groups at equal distances, these features let you do it visually and precisely. You can even align structures to global reference axes or planes via context menus or compass widgets.
Tips and Tricks
- Hold Ctrl (or Cmd) and click on any widget to enter precise numeric values for translation or rotation.
- Use the editor’s context menu (right-click on a widget) to swiftly align selections along global axes.
- Enable grid overlay in the viewport (Z = 0 plane) to help orient large assemblies.
Wrapping Up
Whether you’re modifying a small molecule or assembling a large macromolecular system, SAMSON’s Move Editors offer a highly visual and flexible way to work in 3D. By combining snapping, widget-based manipulation, and integration with alignment tools, they streamline spatial modeling tasks and help reduce guesswork.
To learn more, visit the full documentation 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.