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
When Maintain current aspect ratio is on, the image width/height ratio is constrained to match the width/height ratio of the graphics window (not including borders). Entering the width automatically adjusts the height and vice versa.
When Maintain current aspect ratio is off, both width and height can be set as desired. Grow to Fit resizes the graphics window to match the image aspect ratio by increasing one window dimension (i.e., width or height), while Shrink to Fit resizes the graphics window to match the image aspect ratio by decreasing one window dimension. If the window has not been grown or shrunk to match the image aspect ratio, a saved image will include more than what is displayed.
When dimensions are specified in units of length (anything other than pixels), they are converted to inches internally and multiplied by the Print resolution (dpi) to give the output pixel dimensions. The print resolution setting is saved in the preferences file.
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.Otherwise:
The image will be rendered offscreen 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. 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).
The following pertain to rendering high-quality images directly with Chimera. While raytracing generates shadows and can give a more dramatic appearance, it is often the case that clearer and more illustrative images can be obtained by rendering directly with Chimera.
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. A simple, line-drawing-like appearance can be achieved by combining publication preset #1 or #2 with ambient-only lighting.
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, 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. It can be turned off or its strength adjusted with the Effects tool or the set command, or by moving the global clipping planes. By default, the depth cueing color tracks background color, but can be changed independently with the Color Actions dialog, the Effects tool, or the command set dc_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:
Transparency. Surfaces and other items can be transparent. Rendering only the topmost layer of all transparent items (collectively) rather than multiple layers simplifies the display and is an effective way of de-emphasizing transparent parts. Single-layer transparency is on by default, but can be switched to multiple layers with the Effects tool or the command set.
Shadows and raytracing. Shadowed images can be produced by raytracing with POV-Ray. Shadows can make a scene more dramatic and enhance the sense of depth, but they can also make images harder to interpret by increasing complexity and/or obscuring parts of the scene. Scenes with surfaces may benefit more than scenes containing many smaller objects such as ribbons and sticks. Raytracing can increase time requirements significantly, among other limitations. Some raytracing parameters are controlled independently of the Chimera scene in the POV-Ray Options preferences. If ribbons are raytraced, it may be helpful to show them in the supersmooth style. Alternatives for producing shadowed images are conic and neon (the latter is not available on Windows), and there are also ways to increase shininess without raytracing.
Labeling and other annotation. 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 labels (shown with the Actions... Label menu or commands label and rlabel) are tied to atoms in 3D, and their font and size can only be set collectively, in the Background preferences. The spatial offsets of these “3D” labels can be controlled with label/rlabel and adjusted interactively with the mouse. However, by default (see the Background preferences), they will be drawn in front regardless of their Z-offsets. Spacefilling 3D objects including arrows can be created with the command shape or in BILD format.
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.
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: