The Save Image panel (opened with File... Save Image) allows the contents of the graphics window to be saved as an image file. See the Image Tips for hints on preparing images for saving.
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, width and height can both 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 resized to match the image aspect ratio (as specified by the values entered for width and height), a saved image will include more than what is visible in the display.
Clicking Cancel on the Save Image panel closes it without saving an image. Help opens this manual page in a browser window, while Tips shows the Image Tips section of this manual page.
Clicking Save As dismisses the Save Image panel and initiates redrawing the image in the appropriate size for saving. Because this is generally a different resolution than that shown on the screen, different portions of the image will "flash" within the graphics window. Other windows should not be placed over the graphics window while the image is being drawn.
When the image computation is finished, a dialog for saving the image file will appear; a file name and file type (format) can be specified, or the save can be canceled. The possible formats are PNG, TIFF, JPEG, PS (PostScript), and EPS (Encapsulated PostScript). 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 and stereo PNG. Viewing such files as standard JPEG and PNG shows side-by-side images, but special viewers are available to show them as stereo. For Windows systems, free viewers include JPSViewer LE and NVidia's consumer 3D stereo driver (requires the appropriate graphics hardware).
See also the command copy and exporting a scene.
The Images for Publication tutorial includes step-by-step examples of image creation.
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:
Shininess of stick, ball-and-stick, sphere, and ribbon molecular representations and most surfaces can be adjusted with Shininess Control.
Lighting in Chimera is provided by two light sources. Their positions and intensities can be adjusted in the Lighting tool.
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. Cross-eye stereo images can be saved by setting the Image camera mode in the Save Image panel to stereo pair. Wall-eye and red-cyan stereo images can be saved by first changing the graphics window to the corresponding camera mode with the Camera tool (or the command stereo), then setting the Image camera mode to same as screen. This latter approach is not recommended for cross-eye stereo images because of current problems with that mode in the graphics window.
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.