Rotating part of a molecule can be surprisingly easy to get wrong. A drag may move the whole selection, use an inconvenient axis, or leave you unsure which side of a bond will rotate. When your goal is to adjust a molecular fragment, the Local Move editor offers a more targeted approach: work from the bond, choose the fragment side, and adjust the dihedral angle with its widget.
Start with the fragment, not the whole structure
Load a molecule, then select the atoms you want to work with. For a group of atoms, SAMSON’s rectangle selection editor can help. Before moving anything, check that the selection contains the intended fragment. This simple pause helps prevent a common source of frustration: repositioning more of the molecule than you meant to.
Activate the Local Move editor with the M shortcut. Its widgets are oriented around the selection’s principal axes, which makes it useful when you want to move or rotate selected objects relative to their local orientation. If you instead need to work along the global X, Y, or Z axes, use the Global Move editor (K).
Use the bond to choose what rotates
For a dihedral adjustment, click the half of the bond on the side of the fragment you want to rotate. The editor displays an angle widget for editing the dihedral. That bond-side choice matters: it helps you identify the moving fragment before you make the change.
This is a useful alternative to trying to rotate a fragment freely and then correcting its orientation by eye. The widget gives you a direct way to work with the angle, while the editor’s other controls remain available for broader translations and rotations.
Choose the right control for the job
- Adjust a dihedral: click the appropriate half of the bond and use the angle widget that appears.
- Rotate around a local axis: drag one of the Local Move editor’s curved side widgets.
- Rotate freely: drag the trackball widget.
- Translate along a local direction: use the straight-arrow or plane translation widgets.
The Local Move editor’s colors distinguish its three principal axes: light blue for local X, mid blue for local Y, and dark blue for local Z. If you need to align or move objects relative to the shared global coordinate frame instead, the Global Move editor uses red for X, green for Y, and blue for Z.
Make adjustments easier to repeat
Snapping can make movement and rotation more controlled. You can adjust snapping from the active editor’s quick-access menu in the top-left of the viewport, or in Interface > Preferences > Editors > Snapping. For example, the documentation demonstrates translational snapping at 0.5 Å and rotational snapping at 10°. Choose values appropriate to the adjustment you are making; the examples are starting points, not requirements.
For a drag-based move or rotation, press and hold the relevant widget, move the mouse, then release to apply the change. If the preview is not what you intended, press Esc before releasing to restore the previous position. After applying a move, you can also undo it through Edit > Undo.
A practical sequence is: select the intended fragment, activate the Local Move editor, click the correct half of the bond, inspect the angle widget, and make a restrained adjustment. If you are uncertain about the result, cancel or undo rather than layering additional corrections on top.
For more examples and details on moving, aligning, and distributing objects, see the SAMSON guide to moving objects.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.