The electron density panel contains several view options:
- None - the electron density cloud is not displayed
- Solid - the cloud is displayed as a solid mass, ranging from translucent to opaque based on the "alpha" setting
- Wireframe - the cloud is displayed as a mesh surface, with the protein visible through the spaces in the mesh
- Isocontours - the cloud is displayed as a faint translucent surface marked with bright isocountour lines
- Grid - the cloud is displayed as a faint translucent surface marked with a bright rectangular grid
The "Enable Backface Culling" option, when checked, removes parts of the cloud away from the viewer. The effect of backface culling is most noticeable with the Wireframe, Isocountours, and Grid options. It also affects the appearance of the Solid view options at low settings of the alpha slider.
The Red, Green, and Blue sliders can be used to adjust the color of the cloud.
The Alpha slider controls the overall brightness of the cloud. With the Solid view option, it can be used to change the cloud from translucent to opaque.
The Threshold slider controls the level of density displayed. When the slider is at low value, the cloud is larger because areas of lower density (lower probability of an electron being present) are displayed. With the slider at its highest value, the cloud may disappear or show only in isolated spots.
A medium-high setting of the Threshold slider tends to highlight the protein's backbone, while a medium-low setting may reveal the shape of sidechains.
In addition the view-related options and control, the Electron Density panel has several tools for working with the density.
The Focus on Density button centers the display on the density cloud. This allows the cloud to rotated and zoomed, and not the protein. This option is most useful when the protein is outside of the cloud.
The Center Protein on Density button moves the protein into the density cloud. This option is most useful when the protein has been folded outside the cloud.
The Trim Density button allows the user to trim the density based it's current distance from the protein's backbone. See Electron Density Trim for more.
The Clear Density Notes button removes any density notes. Density notes are created by hovering over the cloud at an interesting spot, and hitting the tab key. A colored dot is added the cloud at the spot. Clicking on the colored dot allows the user to add text describing the spot. Density notes can be helpful in identifying sidechains or structures such as helixes and sheets.
Right-clicking (or command-clicking) on a density note spot lets the user change the color of the spot's dot.
When adding a density note, the spot be away from the protein. Hitting tab while hovering over the protein opens a segment note.