A common modeling frustration is moving the right part of a molecule while leaving the rest untouched. A drag can send a fragment in an unexpected direction, or a rotation can be difficult to control when the molecular axes do not match the screen. In SAMSON, the Local Move editor provides a practical way to translate and rotate a selection relative to its own principal axes—and to edit a bond’s dihedral angle directly.
Start with the right selection
Before moving anything, select the atoms or other movable nodes you want to transform. For a molecular fragment, make the selection deliberately: the editor acts on the selected objects, so checking the highlighted region before dragging helps avoid moving more of the structure than intended. If you need to select a group of atoms, the rectangle selection editor is one option.
Press M to activate the Local Move editor. Its widgets are oriented around the selection’s principal axes, which is useful when the local geometry matters more than the global X, Y, and Z directions. If instead you need motion aligned to the global reference frame, use the Global Move editor with K.
Choose the widget for the motion
- Move in the camera plane: drag the central translation widget, the cross with arrows. This is convenient for placing a fragment visually in the current view.
- Translate along a local axis or plane: use the side translation arrows or plane widgets. These follow the selection’s principal axes rather than the global axes.
- Rotate around a local axis: drag a curved side rotation widget.
- Rotate freely: drag the spherical trackball.
Axis translation follows the selected objects’ local orientation.
The widget colors distinguish the three principal axes: light blue for local X, mid blue for local Y, and dark blue for local Z. This gives you a quick visual cue about which direction a translation or rotation will follow.
Make the movement controlled and reversible
For a precise drag, press the left mouse button on the desired widget, move the mouse, then release to apply the displacement. The editor displays the positional shift while you move. If the result is not what you intended, press Esc before releasing to cancel and restore the previous position. After applying a move, you can also undo it with Edit > Undo.
Snapping can make repeated or measured adjustments easier. Enable translational or rotational snapping from the viewport’s quick access menu, then choose a suitable increment—for example, 0.5 Å for translation or 10° for rotation. The appropriate increment depends on the adjustment you are making; the benefit is that the motion lands on consistent steps instead of relying only on the mouse.
For a bond torsion, use the dihedral control
When your goal is to change a dihedral angle, you do not need to approximate the rotation by dragging the whole editor widget. With the Local Move editor active, click the half of the bond belonging to the fragment you want to rotate. A widget appears for editing the angle. This makes the intended rotating fragment explicit and gives you a direct way to adjust the torsion.
A simple workflow is: select the fragment, activate M, choose the translation or rotation control that matches the task, and use snapping or the dihedral widget when you need more structured control. If you need to align the entire structure to the global XYZ frame instead, the structure’s context menu offers options such as centering on the origin or aligning with a global axis or plane.
For more details on moving, aligning, and distributing objects in SAMSON, see the Moving objects documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.