The Viewing Tool has five sections shown as index cards, Camera, Effects, Rotation, Side View, and Lighting. Only one card is shown at a time, and clicking the tab for another brings it to the front. Close dismisses the Viewing Tool; Help opens this manual page in a browser window.

Camera

The Camera section of the Viewing Tool describes and allows adjustment of the view shown in the graphics window. There are several ways to start Camera, a tool in the Viewing Controls category. Default settings are indicated in bold.

• camera mode (cross-eye stereo/mono/red-cyan stereo/stereo/stereo left eye/stereo right eye/VRex row stereo/wall-eye stereo) - camera mode refers to any of several stereo and mono viewing options. The stereo mode (sequential stereo) may not be available, depending on the system.
• projection (perspective/orthographic) - perspective causes atoms and bonds further from the viewer to appear smaller, and is indicated in the Side View by red lines diverging from the eye position. An orthographic projection has no scaling-with-distance effect, and is indicated in the Side View by horizontal red lines.
• scale factor (1 when a structure is first opened) - a factor reflecting the cumulative effects of scaling with the mouse, the Side View, and/or the command scale
• near plane - Z-coordinate of the front (hither) clipping plane
• far plane - Z-coordinate of the back (yon) clipping plane

Effects

The Effects section of the Viewing Tool describes and allows adjustment of visual effects. There are several ways to start Effects, a tool in the Viewing Controls category. Default settings are indicated in bold.

• depth cueing (on by default) causes regions farther from the viewer to be shaded with the depth-cueing color
  • start ratio (0.5) - how far behind the front clipping plane any decrease in intensity begins, expressed as a fraction of the total distance between the clipping planes
  • yon intensity (0.1) - the intensity of the nominal colors at the back (yon) clipping plane. The intensity decreases linearly from 1.0 at the plane defined by the start ratio to a value of yon intensity at the back clipping plane.
  • color (a color well, black by default) - the color used for front-to-back shading (depth cueing). As the intensities of the nominal colors decrease, the intensity of the shading color increases. When set to No Color, the shading color will be the same as the background color.
• subdivision quality (1.0, maximum 20.0) - the stick, ball-and-stick, sphere, and ribbon representations consist of curved surfaces approximated by collections of planes; increasing the subdivision quality increases the number of planes and the apparent smoothness. If subdivision quality is set to a value below 5.0, it will be raised to 5.0 temporarily when an image is saved. This setting does not affect molecular surfaces.
• local viewer (true/false) - whether for lighting purposes the actual (local) position of the viewer is used. The alternative of treating the viewer as infinitely far away simplifies the lighting calculations and is more computationally expedient. The difference in appearance is generally quite subtle.
• transparent background (true/false) - whether to make the background transparent and allow its opacity to be adjusted (opacity = 1 – transparency). Not all systems have the hardware required to support this option. PNG and TIFF images saved from the session will include opacity information, making them easier to composite with different backgrounds in image-editing applications. (Note: TIFF images with background transparency may not be interpreted correctly by Adobe Photoshop®.) With this option, the opacity is initially set to zero; if the background color is subsequently changed, however, the background will no longer be transparent unless the color definition includes transparency. Background transparency can also be enabled with the startup option --bgopacity.
• silhouette edges (off by default) highlights borders and discontinuities with a thin outline in the silhouette color
  • color (a color well, No Color by default) - when set to No Color, the silhouette color will be gray if the background is black, otherwise black.

Rotation

The Rotation section of the Viewing Tool describes and allows adjustment of rotation parameters. There are several ways to start Rotation, a tool in the Movement category. Default settings are indicated in bold.

• center of rotation method:
  • fixed - uses the rotation center coordinates
  • center of models - sets the center of rotation to the center of the bounding box of all active models (displayed portions only; may include items that are invisible)
  • independent - makes each model rotate around its own center rather than one determined collectively; equivalent to the command set independent
  • center of view - continually adjusts the center of rotation to the current center of view
• rotation center (X, Y, and Z coordinates) - editable only when the center of rotation method is fixed, meaningless when models are set to rotate independently

Side View

The Side View section of the Viewing Tool provides a convenient and intuitive way to scale and to move the clipping planes. There are several ways to start the Side View, a tool in the Viewing Controls category.

The small square on the left represents the viewer's eye position; the two vertical lines represent front and back (hither and yon) clipping planes. Each of these may be moved by dragging with the left mouse button. Dragging the eye position closer to or farther from items in the view scales them up or down, like using the command scale. Dragging either clipping plane is like using the command clip. Dragging the hither clipping plane with the middle mouse button moves both clipping planes in the same direction (like the command section). Dragging the yon clipping plane with the middle mouse button moves the clipping planes in opposite directions (like the command thickness). Simultaneously holding down the Shift key reduces the speed (mouse sensitivity) of such operations by a factor of 10.

Clicking View All adjusts the scale and clipping plane positions so that the view will include everything that is displayed (possibly including items that are invisible ). Model rotations and translations are not adjusted.

A miniature version of the display shows the relationship between the eye position, the displayed item(s), and the clipping planes. By default, the miniature display is shown at high resolution, with colors and representations the same as in the main display. Setting the resolution to low simplifies the miniature to only the backbone of any peptide and nucleic acid residues shown in the main display. In the low-resolution version, surfaces and objects are indicated by bounding box outlines. Low resolution is recommended if performance seems slow when large molecules are being viewed.

The red lines show the field of vision. The use of perspective may be turned off by specifying the orthographic projection (see the Camera section). The Side View will then show parallel rather than diverging red lines.

The clipping planes shown in the Side View act globally. Models can be clipped individually and at any angle using the Per-Model Clipping tool.

Lighting

The Lighting section of the Viewing Tool allows lighting parameters to be changed and saved. There are several ways to start Lighting, a tool in the Viewing Controls category.

In brief, the key light is generally the dominant (brighter) source of light; the fill light serves as a secondary source. Each light includes diffuse and specular contributions. Diffuse light is scattered from a surface equally in all directions, whereas specular light is reflected in a preferred direction. See the discussion of lighting for more details.

The basic lighting interface includes sliders for controlling

• brightness (1.0 by default; possible values range from 0.0 to 5.0)
• key-to-fill ratio (5.0 by default; possible values range from 1.0 to 20.0)

The settings collectively define a scheme that can be named, saved, and later retrieved from the pulldown list indicated by the solid black triangle next to the Lighting field. Choosing a scheme from the list automatically applies it to the view in Chimera. When the name Chimera default is shown, it is only possible to save to a different name, using Save As.... When another name is shown, it is possible to

• Save the current scheme to the name shown
• use Save As... to save the current scheme with a new name
• Delete the scheme whose name is shown

Activating the checkbox marked Advanced opens an interface with additional parameters. In this interface, activating the key light or fill light checkbox lists the corresponding parameters. Default settings are indicated in bold.

• active (true/false) - whether the light is "on." When the key and fill lights are both inactive, the lighting reverts to a single white light aimed along the line of sight.
• diffuse color (a color well, white by default)
• diffuse scale (defaults are approximately 0.861 for the key light and 0.2 for the fill light) - multiplicative scale factor for the diffuse light. Possible values range from -5.0 to 5.0, where negative values result in subtraction of the diffuse light (see the combination rules).
• specular color (a color well, white by default)
• specular scale (defaults are approximately 0.861 for the key light and 0.2 for the fill light) - multiplicative scale factor for the specular light. Possible values range from -5.0 to 5.0, where negative values result in subtraction of the specular light (see the combination rules).
• direction (X, Y, and Z coordinates; by default, approximately -0.383,0.707,0.707 for the key light and 0.259,0.259,0.966 for the fill light) - the apparent source location on a unit sphere with positive X, Y, and Z pointing right, up, and out from the screen.