Electron Density puzzles consist of an unsolved protein and an electron density cloud guide, which has a transparent, globular appearance. The cloud guide is a representation of electrons emanating from the protein structure's amino acids, and provides an insight into what the native structure of the protein will look like, once solved. The guide can alternatively be changed to other viewing modes, including wireframe, and "isocontours" (or "isomesh"). The colour, transparency, density, and viewing mode of the guide can be changed, using settings on the Electron Density panel, available via the shift+e shortcut. The Electron Density panel can be displayed using the shift+e shortcut.
The objective of Electron Density puzzles, is to fit the protein neatly into the protein's electron density cloud, so that little or no part of the protein structure sticks out of the cloud, at a medium density threshold.
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.
These 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-alt-click and drag to adjust near visibility - with the mouse over the background
- use ctrl-shift-click and drag to adjust far visibility - with the mouse over the background
- shift-q to focus on a segment with the mouse over the segment
- Purple dots: open electron density, hover, click. on tab.
- Red, green, or blue dots: right click an existing dot and choose color.
The Electron Density panel can be displayed using the shift+e shortcut in both the original and the selection interfaces. 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.
Getting started - BBF videosEdit
Black Belt Folding Electron videos from 2013
|Karstenw and TimovanderLaan||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.
http://en.wikipedia.org/wiki/Electron_density - Electron Density
http://en.wikipedia.org/wiki/X-ray_crystallography - X-ray Crystallography
http://www.umass.edu/molvis/edm/cloud/ - Interactive Electron Density model (requires Java)