Images can be rendered directly with Chimera or raytraced with POV-Ray using File... Save Image or the copy command. See also: tips on preparing images, making movies, exporting a scene

• EPS - Encapsulated PostScript
• JPEG - see JPEG quality
• PS - PostScript
• PNG (default) - raytracing always produces this format
• PPM
• TIFF - LZW-compressed
• TIFF-fast - uncompressed (larger files)

Additional format options for the stereo pair mode 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 and JPSViewer.

Several dialog settings such as the supersampling level and print resolution are saved in the preferences file.

• Use print units (default off) - whether image width and height are expressed in in physical units of length rather than pixels
• Units (pixels by default, but centimeters/inches/millimeters/points if using print units) - units in which image width and height are specified; all except pixels are units of length (72 points = 1 inch)
  
  
• Image width - image width in units (default is the current pixel width of the graphics window)
• Image height - image height in units (default is the current pixel height of the graphics window)
  
  
• Adjust field of view - when using print units, whether to compute the image field of view from the specified image width instead of the graphics window width. This may provide a better sense of depth.
  • no
  • yes
  • stereo cameras - yes, except when the Image camera mode is same as screen and the graphics window camera mode is mono
  
  
• Maintain current aspect ratio (default on) - whether to constrain the image width/height ratio to match the width/height ratio of the graphics window. If so, changing the image width automatically adjusts the height and vice versa; if not, the width and height can be changed independently. The Grow to Fit button 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.
  
  
• Print resolution (dpi) (default 100.0) - when image dimensions are expressed in print units, they are converted to inches internally and multiplied by this value to give the output pixel dimensions.

• JPEG quality (integer value in the range 5-95, default 90) - quality setting for JPEG output; higher values give larger files
  
  
• Supersample (1x1/2x2/3x3/4x4) - 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 with little effect on file size.
  
  
• Image camera mode - stereo/mono options
  • same as screen (default) - 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 images of views from slightly different angles for combination into a lenticular image; how many images to save is set below
  • stereo pair - regardless of the graphics window camera mode, save a cross-eye stereo pair as 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 image mode instead.)
• Number of lenticular images (default 12) - number of separate images to save when using the lenticular mode. The files will be named by appending a number to the specified file name, before any file type suffix.
  
  
• Raytrace with POV-Ray (true/false) - whether to raytrace with POV-Ray rather than rendering directly with Chimera. If so, the image will be saved in 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 POV-Ray Options button opens the POV-Ray Options preferences.
  
  
• Save temp session in case of image-save crash - whether to save a temporary session file in case of image-saving failure or crash. If there is no failure, the temporary file will be removed automatically; if there is a failure, at the next Chimera startup, the user will be given the option of restoring the session.

Clicking Save dismisses the dialog and initiates saving the image, whereas Close simply dismisses the dialog. Clicking Citing Chimera shows how to credit Chimera, Tips shows the tips on preparing images, and Help opens this manual page in a browser window.

Chimera performs offscreen rendering 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; during this process, the graphics window should not be obscured by other windows or moved offscreen, even partially.

The following mostly pertain to rendering high-quality images directly with Chimera. While raytracing 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. Two categories of presets are available:
    • interactive - for interactive viewing in Chimera
    • publication - for making publication/presentation images
Publication presets make the background white, increase smoothness, and adjust display styles, without changing which items are displayed or their colors. Currently presets cannot be user-defined, but a similar result can be achieved by creating an alias from commands that specify the desired settings.

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.

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. Publication presets #1 and #2 turn on silhouette edges and turn off depth cueing.

Depth cueing is progressive shading from front to back, also known as fog. It can be controlled with the Effects tool or the set command. The depth cueing color tracks the background color by default, but it can be changed independently with the Color Actions dialog, the Effects tool, or the set command. Publication presets #3 and #4 turn on depth cueing and turn off silhouette edges.

Lighting. Chimera lighting modes may include ambient (nondirectional) light and/or up to three directional lights:
    • ambient - ambient-only, giving an unshaded, flat appearance
    • single - single directional light + ambient
    • two-point - two directional lights + ambient
    • three-point - three directional lights
A simple, line-drawing-like appearance can be achieved by combining the ambient mode with publication preset #1 or #2 (white background, silhouette edges). Lighting mode, brightness, contrast, and light directions can be controlled with the Lighting tool and lighting command.

Shininess. Setting quality to glossy in the Intensity section of 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 section. Lighting and shininess can also be adjusted with the lighting command.

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

• Atoms, bonds, ribbons. Display styles other than wire (which is not recommended for publication images) can be smoothed by raising the subdivision quality with the Effects tool or the set command. This setting also affects curved geometric objects defined in BILD format.
  
  
• Surfaces. The smoothness of a molecular surface can be increased by increasing its vertex density with the command setattr, the Selection Inspector, or the molecular surface attributes panel (see also the New Surfaces preferences.) Separate smoothing options are available in Multiscale Models and Volume Viewer for the surfaces they create.
  
  
• Supersampling. The smoothness of edges in saved images can be increased by supersampling, where Chimera automatically saves an image at higher resolution (larger pixel dimensions) than requested and then samples it back down to the requested final size. The default level of supersampling, 3x3, is usually recommended for publication images and gives much smoother edges than no supersampling (1x1). For individual images, the supersampling level is specified in the Save Image dialog or with the copy command's supersample keyword. The command movie record, the Movie preferences, and the MD Movie recording dialog also include supersampling options. Supersampling increases calculation time with little effect on file size. A potential disadvantage of over-supersampling is that lines such as silhouette edges or hydrogen-bond representations in the final images may become unacceptably thin because there is a limit to how wide they can be in the initial images. The File... Save Image dialog reports the effective maximum linewidth. It may be possible to achieve the desired thickness by reducing the supersampling level and/or the pixel dimensions of the image.

• Surfaces (surface models) can be made transparent without otherwise changing their colors using the Actions... Surface menu. Setting quality to glossy in the Lighting tool gives angle-dependent transparency, i.e., makes surface triangles appear more opaque when viewed edge-on; whether this option is available depends on the graphics driver.
  
  
• Atoms, bonds, and ribbons can be made transparent without otherwise changing their colors using the command transparency, or they can be assigned transparent colors directly. These more general approaches also work for surfaces. A transparent color can be defined in the Color Editor and applied using the Actions... Color menu or various coloring commands. Transparent colors can also be specified in commands by name (previously assigned with colordef) or as four comma-separated values (red, green, blue, and opacity components, each in the range 0-1).
  
  
• Geometric objects defined in BILD format can be made transparent with the .transparency directive.

Labels and Arrows. 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. A color key shows how a coloring scheme relates to quantities. Such coloring schemes are applied by various tools, including Render by Attribute. Color keys suitable for publication images can be created with the Color Key tool.

Ribbon path. By default, the ribbon path is a smoothed spline that may deviate from the true positions of the backbone atoms, making bonds to sidechains appear unnaturally short or long (details...). The path calculation can be adjusted with the command ribspline, the molecule model attributes panel, and the Selection Inspector. For proteins, a cardinal spline without smoothing is constrained to pass through α-carbon coordinates, but gives a very rumpled ribbon; a cardinal spline with strand-only smoothing may be a useful compromise.

Shadows and raytracing. Shadowed (noninteractive) 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 “busy” scenes with ribbons and sticks, and raytracing tends to make surfaces very shiny. Raytracing can be quite slow, among other limitations. Apart from raytracing, alternatives for producing noninteractive shadowed images are conic and neon (the latter is not available on Windows), and if system hardware permits, interactive shadows can be enabled with the Effects tool or the set command. There are also ways to increase shininess without raytracing.

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:

• ColorBrewer - multipurpose color-scheme picker; 3- to 12-color schemes are displayed on a map and rated by suitability for red-green colorblind viewers, projection, color printing, black-and-white photocopying, etc.
  (Note: hex color specifications at this site can be converted to Tk codes by replacing the leading 0x with #; for example, hex 0xe78ac3 corresponds to Tk code #e78ac3. In Chimera, Tk codes can be used in coloring commands and entered into the Color Editor.)
• Vischeck - simulates the effects of color-blindness on your own uploaded image or a specified Web page
• IDEA vision demo - simulates several types of color-blindness using images already at the site