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. 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.

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.

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.

Side View

full resolution
low resolution
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.

Light direction can be manipulated interactively within the window containing a sphere; a solid arrow is shown for each active light source, and the arrow representing the currently checked light can be moved along the sphere's surface with the mouse. The outlines on the sphere represent directions that typically give favorable results. See the discussion of lighting for more on lighting directions.

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

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 named scheme designated as the start-up setting will be used for the next session that uses the same preferences file, unless overridden by a session file.