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. Additional files for POV-Ray containing the scene (*.pov) and the raytracing options (*.ini) will be generated and then used to initiate the raytracing calculation. If necessary, the calculation can be halted by clicking Abort on the POV-Ray progress bar.
The image will be redrawn in the graphics window; that is, portions of the image will "flash" within the window, depending on the specified size and degree of supersampling. Other windows should not be placed over the graphics window while this is occurring.

After the image has been redrawn, the file name and type (format) can be specified, or the save can be canceled. Images can be saved in the PNG, TIFF, 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 LE, and NVidia's consumer 3D stereo driver (requires the appropriate graphics hardware).

Tips on Preparing Images

The Images for Publication tutorial includes step-by-step examples of preparing an image in Chimera.

Presets are predefined combinations of display settings. Choosing an entry in the Presets menu applies its settings. Further changes can be made as desired after a preset has been applied. Publication presets make the background white, adjust display styles, and increase the smoothness of curved objects (which may decrease interactive performance).

Background color can be changed using the menu (Actions... Color), the command set bg_color, or the Background preferences. When the background is a light color, a light or matching depth cueing color may be best. If system hardware permits, background transparency can be enabled in 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. Depth cueing can be adjusted by moving the clipping planes or by changing associated parameters including the depth cueing color in the Effects tool. The depth cueing color can also be changed using the menu (Actions... Color) or the command set dc_color.

Clipping planes cut away portions of structures, surfaces and objects. The front and back clipping planes are global (affect everything in the view) and are always perpendicular to the line of sight; they can be moved interactively in the Side View or by using the commands clip, thickness, and section. In addition, there can be per-model clipping planes that only affect individual models and can be placed at any angle. Clipped surfaces can be made to appear solid rather than hollow using Surface Capping.

Smoothness can be increased by increasing the resolution (number of pixels). Additionally, independent of resolution:

Silhouette edges (see the Effects tool) are outlines that can clarify structures by emphasizing borders and discontinuities.

Lighting in Chimera is provided by two light sources. Their positions and intensities can be adjusted in the Lighting tool, along with the shininess of most molecular display styles and surfaces.

Shadowed images. Shadowed images can be produced by raytracing with POV-Ray. Not all of the image tips pertain 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. In scenes with ribbons, the supersmooth ribbon style is recommended for use with raytracing. Although the quality of interactive shadows is currently insufficient for publication images, this option may be useful for previewing where shadows will fall in a raytraced image. Shadowed images can also be generated with conic or neon (the latter is not available on Windows).

Labeling. Labels appropriate for publication/presentation images can be generated with the 2D Labels tool or its command equivalent, 2dlabels. These labels have controllable content, size, and color, and can be placed anywhere in the (X,Y) coordinate system of the graphics window. The standard labels in Chimera (those generated with the Label section of the Actions menu or the commands label and rlabel) have controllable content and color, but there is little control over position. The font and size of standard labels can be adjusted, but only collectively.

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.

UCSF Computer Graphics Laboratory / May 2008