One of the frustrating moments in molecular modeling is trying to adjust a small part of a structure and accidentally moving or rotating more than intended. The key is to separate two decisions: what is selected and which coordinate frame controls the motion. In SAMSON, selecting a fragment and using the Local Move editor gives you a way to work on that part while keeping the rest of the structure in place.
This is useful when positioning atoms for inspection, adjusting a fragment, or changing a dihedral angle. The method below focuses on controlled, reversible edits rather than freehand dragging.
Start with the selection
Load a molecule, then select only the atoms you intend to move. For a group of atoms, the rectangle selection editor can help define the selection in the viewport. Before moving anything, check that the selection contains the intended fragment: a move editor acts on selected objects, so selection is the first control on the scope of the change.
Choose the coordinate frame that matches the task
Press M to activate the Local Move editor. Its translation and rotation widgets follow the principal axes of the selection. That makes it a natural choice when the motion should follow the fragment’s own orientation. By contrast, the Global Move editor, activated with K, uses the global X, Y, and Z axes. The Displacer, activated with D, moves nodes in the camera plane and is useful for straightforward screen-space repositioning.
In the Local Move editor, the central translation widget moves the selection in the camera plane. Side arrows translate along the selection’s principal axes, while curved arrows rotate around those axes. The spherical trackball provides free rotation. These controls make it easier to choose a constrained motion instead of dragging a fragment in an unintuitive direction.
Make a controlled rotation
- Select the atoms that should move.
- Activate the Local Move editor with M.
- For an axis-based rotation, drag the relevant curved-arrow widget. For a free rotation, drag the trackball.
- Watch the displayed motion as you drag. Press Esc to cancel and restore the previous position, or release the mouse button to apply the displacement.
For a dihedral-angle edit, SAMSON provides a more direct interaction: click the half of the bond corresponding to the fragment you want to rotate, then adjust the angle with the widget that appears. This is particularly handy when the task is not “rotate this selected group in space” but “change the relative orientation of the two sides of this bond.”
Use snapping when repeatability matters
Free dragging is helpful for exploration; snapping is useful when you want motion in defined increments. Translational and rotational snapping can be configured in the viewport’s editor quick-access menu or in Interface > Preferences > Editors > Snapping. For example, the documentation demonstrates translation snapping at 0.5 Å and rotational snapping at 10°. These are example values, not universal settings: choose increments appropriate to the adjustment you are making.
You can also enter precise translation or rotation parameters by right-clicking a move-editor widget, or by holding Ctrl on Windows/Linux or Cmd on macOS while left-clicking a widget. Right-clicking widgets also provides commands for aligning objects with global axes.
A small safety habit
Move operations are undoable through Edit > Undo. For a careful workflow, make one deliberate change at a time, inspect the result, and undo if the motion was not what you intended. Keeping the selection focused, choosing local or global axes deliberately, and using snapping only when it helps can make fragment adjustments much less fiddly.
For the complete guide to moving, aligning, and distributing objects, see the SAMSON Moving objects documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.