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 Parameters category. Default settings are indicated in bold.

• camera mode (cross-eye stereo/mono/stereo/stereo left eye/stereo right eye/VRex row stereo/wall-eye stereo) - the stereo mode will only work when --stereo has been specified at the time of Chimera startup.
• 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 Parameters category. Default settings are indicated in bold.

• depth cueing (on by default) causes regions farther from the viewer to be shaded (less intense)
  • start ratio (0.2) - 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 shading (depth cueing). As the intensity of the nominal colors decreases, the intensity of the shading color increases. When set to No Color, the shading color will be the same as the background color (which can be controlled in the Background preferences).
• 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. 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.

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 Viewing Parameters 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 Parameters category. The small square on the left represents the user's eye position, and the two vertical lines represent the hither and yon clipping planes. Each of these may be moved by dragging with the left mouse button. Movement of the eye position closer to or farther from the items being viewed scales them up or down.

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 is shown at full resolution, with colors and representations the same as the main display. Setting 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. Using low resolution is recommended if performance seems slow when large molecules are being viewed.

Dragging the hither clipping plane (the one closer to the eye position) with the middle mouse button moves both clipping planes in the same direction (like using the command section). Dragging the yon clipping plane with the middle mouse button moves the clipping planes in opposite directions (like using the command thickness).

Note that holding the Shift key down will reduce the speed (mouse sensitivity) of manipulations in the main window and Side View by a factor of 10.

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 (on all models). 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 Parameters category.

In brief, the key light is generally the dominant (brighter) source of light; the fill light generally 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.

Activating the checkbox next to key light or fill light 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 0.8 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 0.8 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.

The key and fill light 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