Saving Images

The contents of the Chimera graphics window or a raytraced image from POV-Ray can be saved to a file with File... Save Image. See also: copy, making movies, exporting a scene, tips on preparing images

Clicking Save As dismisses the dialog and initiates saving the image. Cancel dismisses the dialog without saving an image. Help opens this manual page in a browser window, while Tips shows the tips on preparing images.

If raytracing:

Images can only be saved in the PNG format. First, POV-Ray input files containing the scene (*.pov) and raytracing options (*.ini) are generated, and then the raytracing calculation is run as a background job that can be monitored or canceled using the Task Panel.
The image will be rendered offscreen as permitted by the system. (Offscreen rendering is not supported by X11 in Mac OS or by certain older machines with other operating systems. 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. The graphics window should not be obscured by other windows or moved offscreen, even partially, while being used to draw the image.)

After the image has been rendered, the file name and type (format) can be specified, or the save can be canceled. Images can be saved in the PNG, TIFF (LZW-compressed), TIFF-fast (uncompressed), PPM, JPEG, PS (PostScript), and EPS (Encapsulated PostScript) formats. The quality of JPEG files can be specified as an integer in the range 5-95, with higher values corresponding to higher quality and larger files.

Additional format options for stereo pairs are stereo JPEG (*.jps) and stereo PNG (*.pns). 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, JPSViewer, and NVidia's consumer 3D stereo driver (requires the appropriate graphics hardware).

Tips on Preparing Images

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. Publication presets make the background white, adjust display styles, and increase smoothness.

Background color can be changed using the menu (Actions... Color), the set command, (for example, set bg_color white), or the Background preferences. If system hardware permits, background transparency can be enabled with the Effects tool. Images saved with a transparent background are easier to composite with different backgrounds in image-editing applications.

Depth cueing is progressive shading from front to back, also known as fog. Depth cueing can be adjusted by moving the global clipping planes or by changing associated parameters including the shading color with the Effects tool or the set command. The depth-cueing color can also be changed using the menu (Actions... Color).

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.

Silhouette edges are outlines that emphasize borders and discontinuities. Although shown in the interactive display, these are mainly intended for output images (supersampling makes them look much smoother in the image than on the screen). Silhouette edges and their thickness and color can be controlled with the Effects tool or the set command.

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

Shininess. Setting quality to glossy in the Lighting tool makes everything look smoother and shinier; whether this option is available depends on the graphics driver. Even if glossy lighting is not available, specular highlights can be adjusted in the Shininess tool.

Transparency. Surfaces and other items can be transparent.

Lighting. There are two lights in Chimera, key and fill. Their positions and other characteristics can be adjusted in the Lighting tool.

Shadows. Shadowed images can be produced by raytracing with POV-Ray. Not all of the image tips apply to raytracing: some aspects of a Chimera scene are not handled (see raytracing limitations), and some raytracing parameters are controlled independently of the Chimera scene in the POV-Ray Options preferences. The supersmooth style of ribbon is recommended for use with raytracing. Shadowed images can also be generated with conic or neon (the latter is not available on Windows).

Labels. Labels suitable for publication images can be added with the 2D Labels tool (or command 2dlabels). 2D labels containing arbitrary text and/or symbols can be placed or dragged anywhere in the plane of the graphics window, and each can be colored and sized independently. Standard Chimera labels (those shown with the Actions... Label menu or the commands label and rlabel) can be repositioned with the mouse, but their size can only be adjusted collectively in the Background preferences.

Color Keys. Color keys suitable for publication images can be created with the Color Key tool. A color key shows how colors relate to quantities. Such coloring schemes are applied by various tools, including Render by Attribute.

Stereo. Wall-eye, cross-eye, and red-cyan 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 the same as screen Image camera mode in the Save Image dialog. Another way to save cross-eye stereo images is with the stereo pair Image camera mode; in that case, it does not matter what camera mode is being used in the graphics window, but 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.

Color schemes. Several factors should be considered in color scheme design, including what the colors are meant to indicate, how the data are presented, and whether viewers may have color vision deficiencies. Useful Web sites include:

UCSF Computer Graphics Laboratory / August 2009