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

• Image Size:
  • Use print units - allow image size to be specified in units of length rather than pixels
  • Units (pixels by default, but centimeters/inches/millimeters/points if using print units) - units in which the image dimensions are specified; all except pixels are units of length (72 points = 1 inch)
  • Image width - image width in units
  • Image height - image height in units

  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.

• Image Information:
  • Description - text annotation to be placed in the saved image file (does not affect image appearance)
  • Image Credits - open the Image Credits preferences
  • Citing Chimera - show how to cite Chimera

• Raytrace with POV-Ray (true/false) - whether to raytrace with POV-Ray rather than saving the contents of the Chimera graphics window. The POV-Ray Options button opens the POV-Ray Options preferences.

• Supersample (1x1/2x2/3x3/4x4/5x5/6x6) - how many pixels are sampled in the X and Y dimensions for each pixel in the final saved image. Higher values increase the smoothness of edges in saved images and increase calculation time. The supersampling level is saved in the preferences file.

• Image camera mode - camera mode refers to any of several stereo and mono viewing options.
  • same as screen - use the current camera mode of the graphics window for the image. If the mode is sequential stereo, two separate image files (left-eye and right-eye views) will be saved.
  • lenticular - regardless of the graphics window camera mode, save multiple separate image files of views from slightly different angles, for making a lenticular image with apparent depth. The files will be named by appending a number to the specified file name, before any file type suffix.
  • stereo pair - regardless of the graphics window camera mode, save a cross-eye stereo pair in a single image twice as wide as the specified size, optionally using one of the special stereo formats. (To save a wall-eye stereo image, set the graphics window to that camera mode and use the same as screen option instead.)

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. For Windows systems, free viewers include JPSViewer and NVidia's consumer 3D stereo driver (requires the appropriate graphics hardware).

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:

• the smoothness of curves in the stick, ball-and-stick, sphere, and ribbon molecular display styles can be increased by raising the subdivision quality in the Effects tool. If less than 5.0, the subdivision quality will be adjusted automatically to 5.0 temporarily when an image is saved with the Save Image dialog or the copy command.
  
  
• the smoothness of a molecular surface can be increased by increasing its vertex density in the surface attributes panel. Separate smoothing options are available in Multiscale Models and Volume Viewer for the surfaces they create.
  
  
• the smoothness of edges in saved images (but not the interactive display) can be increased by raising the level of supersampling in the Save Image dialog (for movies, this is instead specified in the Frame Options section of Movie Recorder, or with the supersample option of the command movie record).

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. 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.