Saving Images

Images can be rendered directly with Chimera or raytraced with POV-Ray using File... Save Image or the copy command. See also: tips on preparing images, making movies, exporting a scene

The top section of the Save Image dialog contains a file browser for specifying output location, File name, and File type. Formats include:

When the Image type is a stereo pair, the possible formats also include:

Viewing such files as standard JPEG and PNG shows side-by-side images, but special viewers are available to show them as stereo. Free viewers include StereoPhoto Maker and JPSViewer.

Several dialog settings such as the supersampling level and print resolution are saved in the preferences file.

Image Size: Image Options: Image Description - text annotation to be placed in the saved image file (does not affect image appearance). Clicking Image Credits opens the Image Credits preferences.

Clicking Save dismisses the dialog and initiates saving the image, whereas Close simply dismisses the dialog. Citing Chimera shows how to credit Chimera, Tips shows the tips on preparing images, and Help opens this manual page in a browser window.

Chimera performs offscreen rendering as permitted by the system. Offscreen rendering is not supported by certain older machines. On those systems, the image will be redrawn in the graphics window, piece by piece depending on the specified image size and degree of supersampling; during this process, the graphics window should not be obscured by other windows or moved offscreen, even partially.

Tips on Preparing Images

The following tips mainly apply to high-quality rendering directly in Chimera. Images rendered in Chimera are often clearer and more illustrative than those made with the (noninteractive) raytracing option, and can even include shadows.

The tutorials include step-by-step examples of preparing images in Chimera. Many display styles and colors are available.

Presets are predefined combinations of display settings. A preset can be applied by choosing it from the Presets menu or by using the preset command. Further changes can be made after a preset has been applied. Types of presets:
    • interactive - for interactive viewing in Chimera
    • publication - for making publication/presentation images
    • custom - defined by the user in a script, see the Presets preferences
Publication presets make the background white, increase smoothness, and adjust display styles, without changing which items are displayed or their colors. See also: alias

Background color is set to white by the publication presets mentioned above, but can be set to any color with the Color Actions dialog, the background command, or the Background preferences. The latter two can also set the background to a gradient of multiple colors or to an image read from a file. If system hardware permits, images can be saved with a transparent background.

Silhouettes are outlines that emphasize borders and discontinuities. Although shown in the interactive display, these are mainly intended for output images, as supersampling makes them look much smoother in the image than on the screen. Whether silhouettes are shown and their linewidth and color can be controlled with the Effects tool or the set command. Publication presets #1 and #2 turn on silhouettes and turn off depth cueing. Silhouettes can also be combined with depth cueing, as in publication preset #5. This silhouettes setting is global (applies to all models), but when it is on, the silhouettes for an individual model can be toggled with the command setattr, the Selection Inspector, or the molecule model attributes panel.

If outlines are desired but the silhouettes seem to highlight too many contours, a trick is to use the selection outline instead, as it is limited to the perimeters of selected objects. The selection outline color can be changed, e.g to black, in the Selection preferences. Although the linewidth is not adjustable, a thicker line relative to the selected object(s) can be obtained by resizing the graphics window smaller; a large output image can still be obtained by specifying larger dimensions when saving the image.

Depth cueing is progressive shading from front to back, also known as fog or mist. It can be controlled with the Effects tool or the set command. The depth cueing color tracks the background color by default, but it can be changed independently with the Color Actions dialog, the Effects tool, or the set command. Publication presets #3 and #4 turn on depth cueing and turn off silhouettes. Depth cueing can also be combined with silhouettes, as in publication preset #5.

Lighting. Chimera lighting modes may include ambient (nondirectional) light and up to three directional lights:
    • ambient - ambient-only, giving an unshaded, flat appearance
    • single - single directional light + ambient
    • two-point - two directional lights + ambient
    • three-point - three directional lights + ambient
A simple, line-drawing-like appearance can be achieved by combining the ambient-only mode with publication preset #1, #2, or #5 (white background, silhouettes). Lighting mode, brightness, contrast, light directions, and shininess can be controlled with the Lighting tool and lighting command.

Smoothness can be increased by increasing the pixel dimensions of an image (its resolution). Additionally, independent of resolution:

Ribbon path. By default, the ribbon path is a smoothed spline that may deviate from the true positions of the backbone atoms, making bonds to sidechains appear unnaturally short or long (details...). The path calculation can be adjusted with the command ribspline, the molecule model attributes panel, and the Selection Inspector. For proteins, a cardinal spline without smoothing is constrained to pass through α-carbon coordinates, but gives a very rumpled ribbon; a cardinal spline with strand-only smoothing may be a useful compromise (e.g., ribspline cardinal smooth strand).

Shadows. Shadows can make images more dramatic and enhance the sense of depth. However, they can also make images more complex and darken areas of interest; surfaces may benefit more from shadows than would “busy” images with ribbons and sticks. If system hardware permits, interactive shadows can be enabled with the Effects tool or the command set shadows. Shadow locations and darkness are controlled by the lighting directionality and contrast, respectively. Interactive shadows are often good enough for presentation images, and their appearance can be improved by increasing the shadow quality setting in the Effects tool (albeit at the cost of increased graphics memory usage). They can also be used to preview shadow locations for noninteractive rendering. High-quality, noninteractive shadowed images can be produced by raytracing with POV-Ray. Raytracing can be quite slow, among other limitations. Noninteractive shadowed images can also be generated with the commands conic and neon.

Clipping planes cut away portions of structures, surfaces and objects. The global clipping planes shown in the Side View affect all models and can only be perpendicular to the line of sight. In addition, each model can have a per-model clipping plane oriented at any angle. Surface Capping controls whether clipped surfaces appear solid or hollow.

Transparency. By default, only the topmost layer of all transparent items is shown. This is recommended because it simplifies the display and effectively de-emphasizes those parts. Whether a single transparent layer or multiple layers is shown can be controlled with the Effects tool and the command set singleLayer. Transparency is normally angle-dependent, such that transparent triangles (forming objects as well as surfaces) appear more opaque when viewed edge-on than when viewed face-on. However, the angle dependence can be turned off with the Effects tool or the command set flatTransparency.

Labels and Arrows. 2D text, symbols, and arrows of multiple colors and sizes can be added to the display with the 2D Labels tool (or command 2dlabels). Such 2D annotations are drawn in front of any displayed objects and do not move when the objects are moved. By contrast, the standard Chimera “3D” labels (shown with the Actions... Label menu or commands label and rlabel) are associated with atoms and move along with them. The font and size of all 3D labels collectively and whether they should always be drawn in front are set in the Labels preferences.

Geometric Objects. Spacefilling objects including 3D arrows can be created arbitrarily with the command shape or in BILD format. Axes (cylinders), planes (discs), and centroids (spheres) can be defined from sets of atoms using Axes/Planes/Centroids or the command define, and ellipsoids using measure inertia. The PipesAndPlanks tool shows protein helices and strands as cylindrical “pipes” and rectangular-box “planks,” respectively, with thin connectors. Axis, plane, and centroid objects as well as those from shape and measure inertia are surface models, which have the following advantages over the VRML models from BILD format and PipesAndPlanks:

Markers (spheres) can be placed and paths between them drawn with Volume Tracer. Markers are implemented as atoms and thus also respond to the Actions menu and various commands. See also: Cage Builder, Thermal Ellipsoids, hkcage, Nucleotides, Scale Bar

Color Keys. A color key shows how a coloring scheme relates to quantities. Such coloring schemes are applied by various tools and commands, including Render by Attribute, Surface Color, and rangecolor. Color keys suitable for publication images can be created with the Color Key tool or colorkey command.

Stereo. Wall-eye, cross-eye, red-cyan, and green-magenta stereo images can be saved by changing the graphics window to the corresponding camera mode with the Camera tool (or the command stereo) and using Image type: same as screen in the Save Image dialog. Another way to save stereo images is by setting the Image type to stereo pair (cross-eye) or wall-eye stereo pair; in that case, the resulting image will be twice as wide as the specified size.

Color space. Some publications require images to be in the CMYK color space. Chimera currently saves images in only the RGB color space, so a separate application such as Adobe Photoshop® must be used to switch between the two.

Choosing colors. Several factors should be considered in choosing colors, including what the colors are meant to indicate, their distinguishability from each other and from the background, and whether viewers may have color vision deficiencies. Useful web sites include:

See also: Color Editor, Palette Editor

UCSF Computer Graphics Laboratory / August 2015