Electron Density Puzzles consist of an unsolved protein and an electron density "cloud" ("ED cloud"). The ED cloud represents where the electrons of the protein's amino acids are likely to be found. The cloud is determined experimentally, and provides insight into the native structure of the protein.
The goal of Electron Density puzzles is to fit the protein neatly into the ED cloud, so that little or no part of the protein structure sticks out of the cloud.
A segment may have a positive density score even when it lies outside the visible density cloud. Beyond the visible portion of the density, the same cloud repeats invisibly. Segments may end up aligned with in this invisible density cloud.
In some puzzles, such as 1152: Foldit vs. UMich Electron Density Challenge, the entire protein may not fit within the visible portion of the electron density cloud.
The display of the ED cloud is controlled by the electron density panel. Initially, the ED cloud may not be visible. The view options on the electron density panel determine whether the cloud is displayed. The "Center Protein on Density" button on the panel moves the protein into the visible portion of the cloud.
Even with the cloud visible, it can be difficult to see features within it. Adjusting the various view options in Foldit can help reveal the cloud's secrets. Several keyboard shortcuts make it easier to adjust the view. These shortcuts work on Windows and Mac:
- Toggle the Electron Density panel: shift+e
- Use alt-shift-click and drag to adjust the fog (with the mouse over the background)
- Use ctrl-shift-click and drag to adjust far visibility (with the mouse over the background)
- Use ctrl-alt-click and drag to adjust near visibility (with the mouse over the background)
- Use shift-q to focus on a segment with the mouse over the segment
- Density notes: open electron density, hover on density, tab to create dot.
- Density note text: hover and tab on existing dot to open note
- Change density note color: right click (or command-click) on an existing dot and choose color
In the original interface, the Electron Density panel is also available via Actions -> Electron Density. In the selection interface, the Electron Density panel is available via the "Main" menu, or using the shortcut p -> Electron Density.
The "fog" and "far visibility" controls are somewhat similar. The "fog" control gradually fades the more distant part of the protein. All parts of the protein remain visible in the fog. The far visibility control causes the more distant part of the protein to disappear completely.
The "near visibility" control causes the parts of the protein near the view to disappear.
The shift-q shortcut when hovering over a segment focuses on the segment, and cuts away much of the foreground.
The "q" or "home" keyboard shortcuts reset the view options.
Getting started - videosEdit
S0ckrates' Electron Density videos from 2018:
Black Belt Folding (BBF) Electron Density videos from 2013:
|Karstenw and Timo van der Laan||Susume|
Protein crystallograpers course - Fitting page: Fitting refinement and validation
For a list of Electron Density puzzles that have featured on Foldit, see the Electron Density section on the Puzzle Results page.
2016 Nature paper describing the results from Puzzle 1152, the "Foldit vs. UMich Electron Density Challenge", where Foldit players competed against University of Michigan undergraduates, as well as computer algorithms and professional crystallographers. To quote the paper's abstract:
After removal of disordered residues, a team of Foldit players achieved the most accurate structure.
Foldit post referencing 2019 PLOS Biology paper describing results for Foldit puzzles 1572, 1588, 1598, and 1606. In these puzzles, Foldit players competed with both professional expert crystallographers and various computer algorithms. The post states:
In each of the four puzzles, Foldit player solutions had the best balance of plausibility and fit-to-density!