The Viewing Tool

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.


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. See also: stereo, set projection

The horizontal field of view, eye separation, and position of the focal plane relative to the items in view can be changed interactively using the Top View.


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. See also: set


The Rotation section of the Viewing Tool controls rotation behavior. There are several ways to start Rotation, a tool in the Movement category. See also: cofr, set independent

Side View

Side View

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

Simultaneously holding down the Shift key reduces the speed (mouse sensitivity) of dragging operations by a factor of 10.

Clicking View All turns off global clipping and adjusts the scale to include everything that is displayed. Model rotations and translations are not adjusted.

The Clip checkbox indicates global clipping status (on or off). Cap clipped surfaces... brings up the Surface Capping dialog for controlling the appearance of planar caps where surfaces are sliced away.

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.


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:

The key light is generally the brighter source of light; the fill light is secondary and serves to reveal areas that would otherwise be dark (details...).

The lights can be moved interactively by dragging the solid arrows (red for key, green for fill) on the sphere. If a light is turned off, its arrow is not shown. Outlines on the sphere represent directions that typically give favorable results. Only the advanced interface allows turning off a light or placing it behind the sphere.

The Lights (basic) interface includes:

The Lights (advanced) interface contains additional parameters of the current light (either the key light or the fill light, depending on which box is checked). Default settings are indicated in bold. When the advanced interface is shown, only the solid arrow representing the current light can be moved with the mouse, but it can be moved behind the sphere (not possible when the basic interface is shown).

Settings in the Lighting tool 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

Named schemes are saved in the Chimera preferences file, and are only updated with any changes when Save, Save As..., or Delete is used. The settings in effect when a session is saved (whether or not the scheme has a name) are included in the session file.


The Shininess interface controls the specular parameters of viewed items (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.

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.

UCSF Computer Graphics Laboratory / May 2009