A Backbone Pin can hold a segment at a fixed point in space while other tools operate. Foldit has provided a video demonstrating the use of pins.
Each puzzle has at least one pin, whose default location is on the last segment, the N terminal.
Toggling the "Show backbone pins" setting in View Options will reveal pin(s), which are represented by a pushpin icon.
Opening a cutpoint adds another pin, and typically will place the new pin at the end of that chain (numerically highest segment). [See: Quirks and Buggy Behavior for exceptions to this]
Pins with a blue icon can be moved by dragging them to a new position on the protein. A pin cannot be dragged across an open cutpoint, however, as each segment chain is only permitted one pin each.
Pins by default are "unlocked". In the Unlocked state the pin will always point to the right/horizontally (as displayed in the top image). Right-clicking (or Shift+Left-clicking) on a pin icon Locks the pin, leaving it pointing down toward the backbone. These orientations are static, no matter how the camera is moved.
A Locked pin holds the segment in place during certain operations, such as Wiggle, placement of Blueprint Building Blocks, or Idealize Secondary Structure. Similar to an unlocked pin, a locked pin will
Some puzzles, such as the Aflatoxin puzzles, have locked segments and permanent cutpoints. Puzzles of this type may have fixed pins, which have a gray icon, and which can't be moved or unlocked.
Pins do not affect the operation of the Move tool. A section of the protein, with a cutpoint or a N or C terminal on either end, can be moved freely with a locked pin in place.
The feedback new Pins feature not as expected gives further background on how pins work.
There is no command to lock or unlock all pins. Pins can't be deleted. Closing a cutpoint removes one pin, and may move any remaining user pins. The initial pin (and any fixed pins) cannot be removed.
There are currently no recipe functions to interact with pins. Adding a cutpoint in a recipe adds a pin, but there is no way to control the pin's position or locked/unlocked status.
Quirks and Buggy Behavior
There are instances where the new pin may not turn up at the default location. Typically that only happens when having previously moved the pin. In which case, the new pin in that chain will occupy the prior-pin's location. This is similar to when closing cuts, whereby the pin will appear to move as dictated by wherever the new "end segment" is of that chain. However, this is not where the pin actually resides, contrary to what the UI is showing you! In both cases, be it when creating a cut or closing a cut, where the pin(s) display as being somewhere else, are instances of "Phantom Pin" behavior.
A Phantom Pin is where the visual representation of the Pin(s) does not match with where the game's engine has registered the Pin(s). This can lead to your protein behaving in ways that are completely counter-intuitive to everything explained on this page. Examples of this behavior are the protein rotating around a point other than where the pin is located when using Wiggle, or, the place you are Pulling on is not moving very little or not at all. Again, this is because the pin(s) actual location is being incorrectly represented by the UI.
To sort out an instance of Phantom Pin(s), simply left-click on the pin and this will trigger Foldit to update the pin location(s), revealing any or all pins to shift. It is best practice to click on a Pin multiple times after having closed cuts, in order to cycle through all of the Phantom Pin locations.
WARNING: Be mindful to note that any prior location where you had a Locked Pin, that it will once again be in the Locked state once the location cycles back to that point. (A 'locked' Phantom Pin that is not the current pin location, should not impact tools in the same way as a normal locked pin; best to unlock any you come across just in case.)