The idea is that the protein is being observed through a camera, and moving the camera doesn't change the protein. The protein remains at rest at a point in space.
The protein can also move through space. For example, the Move tool can move all or part of the protein through space. The Pull tool can bend the protein, again moving at least part of it through space. The Wiggle tool can also cause the protein to move, sometimes quite dramatically. Using Bands combined while wiggling usually causes the protein to move.
Unlike moving the view using camera controls, all of these moves through space potentially change the protein's score.
The basic camera controls in Foldit are similar to those in other protein viewers. For the most part, the camera controls are invisible, meaning there are no on-screen graphic elements showing camera position. Most of the camera controls are accessed by dragging on the background while holding various key combinations.
Restoring Visibility, Changing FocusEdit
The camera controls can point the camera pointing at spot where's no protein. Even without camera adjustments, a simple wiggle can cause the protein to leave the spot where the camera is pointing. There are a few ways to get the protein back in view.
Many camera controls involve dragging, often while holding a combination of keys, so simply dragging in the opposite direction with the same key combination can bring the protein back into view.
There are also two hotkeys that can help bring the protein into view.
The hotkey 'q' has two functions. With the mouse on the background, 'q' re-centers the protein in the Foldit window, and resets the visibility and fog (discussed below) to their default values.
With the mouse hovering over a segment of the protein, 'q' centers the camera on the segment and zooms in on it. The related 'shift-Q' hotkey does the same, but also adjusts the visibility settings.
On Windows, the Home key is similar to 'q', but also resets the zoom level. This can be helpful if the camera has zoomed out too far. The Home key also seems to move the camera to its original position in space, similar to resetting the puzzle.
Unlike a manual save, a Quicksave doesn't include the camera position. Restoring a quicksave won't bring a missing protein back.
Changes to the camera's position don't change the score, so the Undo command won't fix an invisible protein.
While many puzzles consist of a single protein chain, other puzzles may have multiple chains or different types of molecules, which move separately in space. In extreme cases, it's possible for these separate pieces to be so far apart in space, that 'q' and Home won't bring them into view. In these cases, it may be necessary to hunt for the protein using the zoom and move controls described below.
The simplest camera control is rotation. Clicking on the background, away from the protein or other molecule, and dragging rotates the camera around the protein. While the protein appears to be turning in the direction of the drag, it can be important to remember that it's actually the camera that's moving, in the opposite direction.
Clicking on the edge of the screen and dragging around the edge of the screen will rotate the camera's orientation while keeping it in place, effectively spinning your 2D view.
The camera is actually moving in a curved path, around a fixed or variable pivot point.
Rotating generally keeps the protein in view, but the 'q' or Home hotkeys can help when rotating has undesired side effects.
Fixed/variable camera pivotEdit
By default, Foldit uses a setting called "fixed camera pivot", meaning the camera rotates around a point that's the approximate center of mass of the protein and other molecules.
In General Options, unchecking the "fixed camera pivot" option means the camera rotates around a point where the pointer was recently positioned. This can be useful in symmetry puzzles, where the symmetric chains may be far apart in the initial design phase. With fixed camera pivot selected, rotating the chain that's being designed tended to move it off the screen. The alternate could be called "variable camera pivot", making it easier to keep the desired piece of protein in view.
Variable camera pivot is also useful in small molecule design puzzles and reaction design puzzles, where a ligand is being designed. Keeping the ligand distant from the protein can be helpful early on.
Similarly, in binder puzzles, having the binder far away from its target is often a useful strategy.
Moving the camera involves holding down the control key and dragging on the background. Control-dragging left makes the protein appear to move left as the camera moves right. Control-dragging right, up, and down produce similar apparent motion, opposite the actual camera motion.
Unlike rotation, control-dragging on the background moves the camera in a straight line, so there's no pivot point.
Moving the camera may mean the protein is no longer visible on the screen. As discussed above, the 'q' and Home hotkeys help make the protein visible again.
Zooming means holding down the shift key and dragging on the background. Dragging upward zooms out, making the protein appear smaller as the camera moves away. Shift-dragging zzooms in, moving the camera closer to the protein. Shift-dragging right and left has no effect.
It's possible zoom out so far that the protein is a tiny speck or even entirely invisible. The 'q' shortcut may help, but the the Home key on Windows also resets the zoom level, helping to resolve this issue.
Fog/Near visibility/Far visibilityEdit
The fog and visibility controls don't move the camera or the protein, but they do affect the appearance of the protein, and they can even make the protein disappear. Similar to rotating, moving, and zooming the camera, they are accessed by dragging on the background. All three controls involve holding down combinations of the shift, control, and alt keys.
The fog control involves holding down the control and shift keys while dragging on the background. As the name implies, the protein gradually fades into a "fog". Dragging downward brings the fog closer to the camera. It's possible to lose the protein in the fog. Dragging upward gradually pushes the fog into the distance. The 'q' shortcut or the Home key also clear the fog.
By default, there's a small amount of fog. Shift-dragging upward on the background allows clearing the fog entirely.
Near visibility and far visibility are similar to the fog, but have a sharp cutoff.
Near visibility works by holding down the control and alt keys, and dragging on the background. Dragging upward cuts off the nearer parts of the protein, until the protein eventually disappears. Control-alt-dragging downward restores visibility, starting the more distant parts of the protein.
Adjusting far visibility involves holding control the control and shift keys, and dragging on the background. Dragging downward cuts off the farther parts of the protein, until the nearest visible parts eventually disappear. Control-shift dragging upward gradually brings the protein back, starting with the parts closest to the camera.
Adjusting near visibility and far visibility is often useful in electron density puzzles, or when making images for sharing.
Electron density puzzles include an electron density "cloud" that can be displayed as a guide to protein folding. The electron density panel has on-screen controls that affect the appearance of the cloud.
The 'shift-Q' hotkey is especially useful in electron density puzzles. As in any puzzle, 'shift-Q' focuses on a segment, zooms in, and adjusts the near and far visibility. The visibility settings also cut away electron density.