You zoom in on a binding site, rotate to inspect a residue, and suddenly the structure is nowhere in the viewport. It may not be gone—you may simply have moved the camera away from the part of the scene you meant to inspect. This is a common frustration when navigating large or dense molecular systems, especially when a small adjustment sends the view off-center.
A useful recovery habit is to treat the camera as part of your workflow, not just a window onto the structure. In SAMSON, the camera determines what you see, and each document contains at least one camera. You can navigate with the mouse, trackpad, or keyboard, and recenter the view when you lose your bearings.
First, choose an editor that fits the task
The active editor determines what viewport interactions do. For general exploration, the View Editor (V) is a straightforward choice: drag with the left or right mouse button to rotate, use the middle mouse button to pan, and scroll to zoom. On a trackpad, use a single-finger drag to rotate, a pinch to zoom, and Shift+Ctrl or Shift+Cmd with a drag to pan.
If you need to select objects while exploring, use the Point Selection Editor (P). Its navigation controls are the same as the View Editor, with selection added on click. You can switch editors from the toolbar at the left of the viewport, use their keyboard shortcuts, or press Esc to return to your default editor.
Use centering as a reset, not a last resort
If the system slips out of view, press Shift+Space. When an atom or other part of the structure is selected, the camera centers on that selection. With nothing selected, it centers on the full molecular system in the active document. This makes the shortcut useful both for recovering the overall scene and for returning to a specific region.
For a closer inspection, select an atom and center on it before rotating. The camera then rotates around that focus, which can make it easier to examine nearby structure without repeatedly losing the point of interest. If you prefer the mouse, the Rectangle Selection Editor supports centering by double-clicking the mouse wheel. In that editor, Shift+Space also centers on the selection—or the full view when there is no selection.
Make depth easier to read
In a dense structure, finding the right camera angle may not be enough: atoms in front of or behind the region of interest can obscure what you want to see. SAMSON’s progressive clipping gradually fades parts of the structure according to their distance from the camera, rather than cutting them off abruptly. It is activated by default.
To adjust the clipping distance, hold Ctrl on Windows or Linux, or Cmd on macOS, while scrolling or sliding on the trackpad. To change the thickness of the visible region—the viewing slab controlled by clipping and fog—hold Shift together with Ctrl or Cmd while scrolling. You can also open the clipping control panel using the clipping and fog icon at the bottom of the viewport. The panel lets you adjust clipping and fog distances; its settings include presets for progressive or traditional sharp clipping, as well as border size.
Keep useful views close at hand
When you need to move between a whole-protein view and a close-up, consider using multiple cameras in the same document. Only one camera is active at a time, but each can preserve a different view. Double-click a camera in the Document view to activate it, or right-click and choose Set as active camera. Add another through Visualization > Camera. This can reduce the need to repeatedly rebuild a view while switching between inspection scales.
A simple recovery sequence is: return to the View Editor, press Shift+Space to regain the full scene, select the region you want to inspect, center again, then adjust clipping if depth makes the area hard to read. If you routinely need two scales, keep them as separate cameras.
For the complete navigation reference, see Moving around in SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.