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.

For just the section being shown: Reset replaces the current settings with the original "factory" defaults, Restore replaces the current settings with those previously saved in the preferences file, and Save saves the current settings to the preferences file. Close dismisses the Viewing Tool, and Help opens this manual page in a browser window.

Camera

The Camera section of the Viewing Tool controls several aspects of the view, including stereo parameters. There are several ways to start Camera, a tool in the Viewing Controls category. Default settings are indicated in bold.

• camera mode (mono/stereo left eye/stereo right eye/cross-eye stereo/wall-eye stereo/red-cyan stereo/sequential stereo/DTI side-by-side) - the camera mode refers to any of several stereo and mono viewing options. Sequential stereo is not always available. For stereo viewing, the DTI mode requires DTI technology.
• reverse sequential stereo (true/false) - whether to reverse the eye views when in the sequential stereo camera mode (to compensate for the reversal introduced by certain devices); can also be specified with the startup option --reverse-stereo. This option does not switch the camera mode.
• 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
• horizontal field of view (allowed range 1.0-179.0°) - how much perspective is used; does not affect the orthographic projection. The vertical field of view will change along with the horizontal field of view, but their exact relationship depends on the aspect ratio of the graphics window.
• Stereo parameters
  • units (millimeters/centimeters/inches) - units for the following stereo parameters
  • eye separation (2.0 inches) - effective distance between the left and right eyes
  • distance to screen - effective distance from the viewer to the screen (or focal plane, even though objects out of this plane do not appear "out of focus"). When viewed in stereo, objects in front of the focal plane will appear to project from the screen, and objects behind the plane will appear to recede behind the screen.
  • screen width - physical width of the entire screen (not just the graphics window). The value is initially what is reported by the windowing system, but it can be edited. Changing the value does not resize the graphics window.

  The eye separation and distance to screen govern the parallax between the left- and right-eye views. The horizontal field of view, distance to screen, and screen width are interdependent. The graphics window width is determined from the screen width and the known pixel dimensions of the screen and graphics window. The horizontal field of view is computed from the graphics window width and the distance to screen. For a given graphics window width, the horizontal field of view and distance to screen are inversely related; changing one changes only the other, in the opposite direction. Changing the screen width or resizing the graphics window changes only the horizontal field of view, in the same direction.

Effects

The Effects section of the Viewing Tool controls visual effects such as depth cueing. 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, No Color by default) - the color used for front-to-back shading (depth cueing). When set to No Color, the shading color will be the same as the background color.
• silhouettes (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.
  • width (1.0) - silhouette linewidth

• 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. If less than 5.0, the subdivision quality will be adjusted automatically to 5.0 temporarily when an image is saved with the Save Image dialog or the copy command.
• 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. For background transparency in raytraced images, see the POV-Ray Options preferences.
• show shadows (true/false) - display interactive shadows to enhance 3D perception during interactive use and/or to preview shadow locations before saving a raytraced image. The appearance of these interactive shadows is fairly rough, so for saving images, raytracing is recommended instead. ** On Mac OS 10.4 (PPC, Intel) and 10.5 (PPC): do not turn on interactive shadows in the X11 version of Chimera, as this has been observed to freeze the display. **
• multisampling (true/false) - whether to use multiple samples per pixel so that edges are antialiased (the default setting depends on the graphics card). Most modern graphics cards support multisampling, although certain graphics driver bugs may necessitate turning it off. Multisampling can also be enabled with the startup option --multisample.

Rotation

The Rotation section of the Viewing Tool controls rotation behavior. 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 yellow square on the left represents the viewer's eye position. Dragging it with the left mouse button adjusts the scale factor (like the command scale). This does not change the stereo parameter distance to screen. Double-clicking the eye position brings up a menu for changing the camera mode.
  
  
• The vertical yellow lines represent the front and back (hither and yon) global clipping planes. Each can be dragged with the left mouse button (like using the command clip). Dragging the hither plane with the middle mouse button moves both clipping planes in the same direction (like the command section), while dragging the yon plane with the middle mouse button moves the clipping planes in opposite directions (like the command thickness). These clipping planes act globally; however, models can be clipped individually and at any angle using Per-Model Clipping.
  
  
• The red lines emanating from the eye position show the field of vision. The lines diverge when perspective is used, but are parallel in the orthographic projection.

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

The default View is right: it shows the relationship between the viewer and the Chimera scene from the viewer's right side. Setting View to top switches to a top view in which stereo parameters and perspective can be adjusted interactively.

By default, the miniature display of the Chimera scene is shown at high resolution, with colors and representations the same as in the main display. Using low resolution simplifies the miniature to molecule chain traces and surface/object bounding box outlines. Low resolution is recommended if performance seems slow with larger systems.

Cap clipped surfaces... draws planar caps where surfaces are clipped away and brings up the Surface Capping dialog to allow further adjustments.

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. The interface can be switched among Lights (basic), Lights (advanced), and Shininess.

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

In brief, the key light is generally the dominant (brighter) source of light; the fill light serves as a secondary source. Each light can include 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 lighting details).

Lighting directions can be manipulated interactively in the small window containing a sphere. Unless turned off, each light source is shown with a solid arrow (red for key, green for fill) that can be moved with the mouse. Outlines on the sphere represent directions that typically give favorable results. Only the advanced interface allows a light to be turned off or placed behind the sphere.

The Lights (basic) interface includes sliders for controlling

• brightness (default 1.0; slider values range from 0.1 to 5.0) - total illumination of the scene
• key-to-fill ratio (default 2.0; slider values range from 1.0 to 20.0) - what proportion of the total illumination is contributed by each light

• 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 0.653 for the key light and 0.500 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 1.0 for the key light and 0.0 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). A light with a specular scale of 0 will be treated as shadowless during raytracing.
• 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.

Shininess

The Shininess interface controls the specular parameters of objects (rather than light sources): shininess, brightness, and the color used for shiny highlights. Although part of the Lighting tool, Shininess is also handled as a separate tool in the Viewing Controls category.

• shininess (30 by default; ranges from 1 to 128) refers to the "spread" of highlights; lower values yield larger, more diffuse highlights, while higher values yield more pointlike highlights. Technically, shininess is the OpenGL specular exponent. The effective highlight intensity varies as the cosine of the angle between the view direction and the direction of the reflected light, raised to the power of this exponent.
• specular color (a color well, a light gray by default) is the color used for shiny highlights. It is added to the color that would be shown in the absence of highlights. If the color is already bright white, highlights will not be discernable; if the color is nominally green and the specular color is red, the highlights will appear to be yellow. This explanation assumes that all light sources are white or gray; however, lights have their own diffuse and specular colors, which must be combined with that of the material.
• brightness (1.0 by default; ranges from 0.1 to 10) scales the intensity of the specular color components, and the resulting values may exceed 1.

The Shininess interface adjusts the material properties of the Chimera default material. Stick, ball-and-stick, sphere, and ribbon representations and MSMS molecular surfaces use the default material. It is not possible to independently control the shininess of different models that use the default material. Except for surfaces generated by Volume Viewer and Multiscale Models (for which special code was written), the properties of models that do not use the default material (VRML models, for example) are not adjusted.