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Wiggle all

The wiggle tools in the action bar allow wiggling both backbone and sidechains (W), sidechains only (E), or backbone only (T). If nothing is selected, the action bar icons say "ALL", and wiggle affects the entire protein

Wiggle selected

Here, one or more segments are are selected, and wiggle affects only these segments. The word "ALL" is not present in the action bar icons.

Wiggle automatically seeks better backbone and sidechain positions.

Along with Shake, Wiggle is one of the most frequently used tools in Foldit.

Wiggle is available on the action bar and via hotkeys. In most puzzles, three wiggle actions are available:

  • wiggle backbone and sidechains (hotkey W)
  • wiggle sidechains only (hotkey E)
  • wiggle backbone only (hotkey T)

The toolbar icons for the different wiggle actions are similar, but the "wiggle sidechains" option contains the letters "SC", while the "wiggle backbone" option contains the letters "BB".

If nothing is selected, the wiggle toolbar icons contain the word "ALL", indicating that Wiggle will affect all segments in the puzzle. When one or more segments are selected, the wiggle icons don't contain "ALL", and wiggling affects only the selected segments.

On small molecule design puzzles, only the "wiggle backbone and sidechains" option is available.

Wiggle is affected by the wiggle power setting in the Behavior Options menu. Lower wiggle power means faster wiggles, but less precise results.

Stop Timer Counter

The timer/counter appears in the lower left corner of the Foldit window while Wiggle and other tools are running. The timer shows the approximate time the tool has been running. The counter shows the number of cycles the tool has completed. Wiggle usually requires multiple cycles to be effective. Clicking the red X stops wiggle.

Both Wiggle and Shake show the counter/time in the lower left corner of the Foldit window. Unlike shake, wiggle requires a variable number of cycles. Shake usually completes its work in the first cycle. There's no precise definition of what a "cycle" is for either Wiggle or Shake.

Unlike Shake, Wiggle can change the shape of the backbone. If there are large clashes or other problems, wiggle can cause the protein to fly apart. Various techniques, including freezing and banding, can be used to help prevent drastic changes during a wiggle. Lowering the Clashing Importance temporarily may also help to avoid the exploding protein syndrome.

Technical details: free energy, the energy landscape, and minimizers

As always, the goal is to improve the Foldit score. Improving the Foldit score involves reducing the protein's free energy. Foldit relies on the underlying Rosetta software, which estimates the free energy, and provides the score. Rosetta also supplies a tool called an energy minimizer, which can be configured in many different ways. The Wiggle tool in Foldit uses the Rosetta energy minimizer.

The way an energy minimizer works involves a lot of very technical details, but a simple analogy is used to explain it.

A protein has an energy landscape, full of hills, valleys, and potholes. The goal of a minimizer is to find the lowest spot in the energy landscape, the point with the lowest free energy. The energy landscape is quite large, so exploring the entire terrain is not generally a good option. A good minimizer tries to be efficient in how it explores. Also, the landscape is invisible, so the minimizer must feel its way around, checking the free energy at each point.

A series of blog posts by Foldit scientist bkoep describe the energy landscape concept in more detail. These posts include:

Wiggle works by making small random changes, and following the energy landscape "down", decreasing the free energy and increasing the Foldit score. Wiggle allows for behavior adjustments, such as Wiggle Power and Clashing Importance.

As it follows the energy landscape, Wiggle can get stuck at a point of stability in the landscape, a low valley or a pothole. Wiggle reached this low spot, but it can't wiggle its way back up and out.

Once Wiggle gets stuck, there are several options which can be used before wiggling again:

Local Wiggle

Local Wiggle is another type of wiggle. Local Wiggle is also a Rosetta energy minimizer, but it uses a slightly different algorithm for exploring the energy landscape.

As usual in Foldit, the exact details are not known, but as the name suggests, Local Wiggle may be better at exploring small, "local", changes to the protein, while regular Wiggle may attempt larger "non-local" changes.

Unlike regular Wiggle, Local Wiggle does not have action bar icons or hotkeys, meaning it can only be used in recipes. (The Foldit original interface may have allowed for manual Local Wiggle.)

In an effort to put Local Wiggle to work, sirenbrian and other Foldit players developed Local Wiggle Strategy, which involved using local wiggle on small sections of protein. Many endgame "LWS" recipes use variations on this strategy.

Recipe interfaces

Wiggle and Local Wiggle are available in recipes.

For regular Wiggle, the functions structure.WiggleAll and structure.WiggleSelected are available. Both functions accept true/false boolean arguments that control whether the backbone and the sidechains are wiggled.

For Local Wiggle, the Lua functions are structure.LocalWiggleAll and structure.LocalWiggleSelected. Again, both functions accept arguments that control wiggling backbone and sidechains.

External links

Wiggle in Foldit is based on Rosetta minimizers. Articles on rosettacommons.org describe minimizers in great detail, but tend to assume the reader is already very familiar with the topic. Here are two examples:

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