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)

When the Image type is a stereo pair, the possible formats also include:

• Stereo JPEG (*.jps)
• Stereo PNG (*.pns)

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 (no/yes/stereo cameras) - 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. The stereo cameras setting (default) indicates making the adjustment for stereo modes only (not when the Image type 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, image 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) - number of pixels per inch in the final image; image dimensions in print units are converted to inches internally and multiplied by the dpi to give the output dimensions in pixels

• JPEG quality (integer value in the range 5-95, default 90) - quality setting for JPEG output; higher values give larger files
  
  
• Rendering:
  • Chimera (default) - Chimera rendering, normally offscreen (details...). Images can be supersampled, that is, initially generated at a higher resolution and then sampled down to the final size.
  • POV-Ray - raytrace with POV-Ray rather than rendering directly with Chimera. Raytracing can be very slow but includes fancier effects such as high-quality shadows. 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. Raytraced images are saved in PNG format.
  
  
• Supersample (1x1/2x2/3x3/4x4) - for Chimera rendering, how many pixels to sample in the X and Y dimensions for each pixel in the final saved image. 1x1 corresponds to no supersampling. Higher values increase the smoothness of edges in saved images and increase calculation time with little effect on file size. 3x3 is generally recommended when supersampling is done. A potential disadvantage of supersampling is that lines such as silhouettes may become unexpectedly thin in the final image because there is a system-dependent limit on how wide they can be drawn in the initial image. The effective maximum linewidth is reported at the bottom of the dialog. It may be possible to achieve the desired linewidth by reducing the supersampling level and/or the pixel dimensions of the image.
  
  
• Image type - stereo/mono options for Chimera rendering
  • 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
    • Lenticular images (default 12) - how many images to save in the lenticular mode. 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 as a single image twice as wide as the specified size, optionally using a stereo format
  • wall-eye stereo pair - regardless of the graphics window camera mode, save a wall-eye stereo pair as a single image twice as wide as the specified size, optionally using a stereo format
  
  
• Transparent background - whether to include opacity values (alpha) in the output file (PNG or TIFF only), to facilitate combining the image with different backgrounds in image-editing applications. With background transparency, if the Chimera background is a single solid color, it will be completely invisible in the saved images. (Note: TIFF images with background transparency may not be interpreted correctly by Adobe Photoshop.) Background transparency can also be enabled with the command set bgTransparency or the startup option --bgopacity. For background transparency in raytraced images, see the POV-Ray Options preferences.

Clicking Save dismisses the dialog and initiates saving the image, whereas Close simply dismisses the dialog. 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 tips mainly apply to high-quality rendering directly in Chimera. Images rendered in Chimera are often clearer and more illustrative than those made with the (noninteractive) raytracing option, and can even include shadows.

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. Types of presets:
    • interactive - for interactive viewing in Chimera
    • publication - for making publication/presentation images
    • custom - defined by the user in a script, see the Presets preferences
Publication presets make the background white, increase smoothness, and adjust display styles, without changing which items are displayed or their colors. See also: alias

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, images can be saved with a transparent background.

Silhouettes are outlines that emphasize borders and discontinuities. Although shown in the interactive display, these are mainly intended for output images, as supersampling makes them look much smoother in the image than on the screen. Whether silhouettes are shown and their linewidth and color can be controlled with the Effects tool or the set command. Publication presets #1 and #2 turn on silhouettes and turn off depth cueing. Silhouettes can also be combined with depth cueing, as in publication preset #5. This silhouettes setting is global (applies to all models), but when it is on, the silhouettes for an individual model can be toggled with the command setattr, the Selection Inspector, or the molecule model attributes panel.

If outlines are desired but the silhouettes seem to highlight too many contours, a trick is to use the selection outline instead, as it is limited to the perimeters of selected objects. The selection outline color can be changed, e.g to black, in the Selection preferences. Although the linewidth is not adjustable, a thicker line relative to the selected object(s) can be obtained by resizing the graphics window smaller; a large output image can still be obtained by specifying larger dimensions when saving the image.

Depth cueing is progressive shading from front to back, also known as fog or mist. 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 silhouettes. Depth cueing can also be combined with silhouettes, as in publication preset #5.

Lighting. Chimera lighting modes may include ambient (nondirectional) light and 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 + ambient
A simple, line-drawing-like appearance can be achieved by combining the ambient-only mode with publication preset #1, #2, or #5 (white background, silhouettes). Lighting mode, brightness, contrast, light directions, and shininess can be controlled with the Lighting tool and 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 level with the Effects tool or the set command. This setting also affects curved geometric objects defined in BILD format. The publication presets increase subdivision to 5.0 if the current value is lower.
  
  
• 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). This parameter can also be specified when a surface is displayed with the surface command. The publication presets raise vertex density to 10.0 for any existing molecular surfaces with lower values. Separate smoothing options are available in Multiscale Models and Volume Viewer for the surfaces they create (see also the command sop smooth).
  
  
• 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 and dialogs for recording movies also include supersampling options. Supersampling increases calculation time with little effect on file size. A potential disadvantage of supersampling is that lines such as silhouettes or hydrogen-bond representations may become unexpectedly thin in the final image because there is a system-dependent limit to how wide they can be drawn in the initial image. The File... Save Image dialog reports the effective maximum linewidth given the current supersampling level and image size. It may be possible to achieve the desired linewidth by reducing the supersampling level and/or the pixel dimensions of the image.

Shadows. Shadows can make images more dramatic and enhance the sense of depth. However, they can also make images more complex and darken areas of interest; surfaces may benefit more from shadows than would “busy” images with ribbons and sticks. If system hardware permits, interactive shadows can be enabled with the Effects tool or the command set shadows. Shadow locations and darkness are controlled by the lighting directionality and contrast, respectively. Interactive shadows are often good enough for presentation images, and their appearance can be improved by increasing the shadow quality setting in the Effects tool (albeit at the cost of increased graphics memory usage). They can also be used to preview shadow locations for noninteractive rendering. High-quality, noninteractive shadowed images can be produced by raytracing with POV-Ray. Raytracing can be quite slow, among other limitations. Noninteractive shadowed images can also be generated with the commands conic and neon.

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.

Transparency. By default, only the topmost layer of all transparent items is shown. This is recommended because it simplifies the display and effectively de-emphasizes those parts. Whether a single transparent layer or multiple layers is shown can be controlled with the Effects tool and the command set singleLayer. Transparency is normally angle-dependent, such that transparent triangles (forming objects as well as surfaces) appear more opaque when viewed edge-on than when viewed face-on. However, the angle dependence can be turned off with the Effects tool or the command set flatTransparency.

• Surfaces (surface models) can be made transparent without otherwise changing their colors using the Actions... Surface menu or the command transparency.
  
  
• 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. Spacefilling objects including 3D arrows can be created arbitrarily with the command shape or in BILD format. Axes (cylinders), planes (discs), and centroids (spheres) can be defined from sets of atoms using Axes/Planes/Centroids or the command define, and ellipsoids using measure inertia. The PipesAndPlanks tool shows protein helices and strands as cylindrical “pipes” and rectangular-box “planks,” respectively, with thin connectors. Axis, plane, and centroid objects as well as those from shape and measure inertia are surface models, which have the following advantages over the VRML models from BILD format and PipesAndPlanks:

• they better handle transparency and/or interactive shadows
• they can be recolored with the Actions menu, color, or scolor

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

Stereo. Wall-eye, cross-eye, red-cyan, and green-magenta 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 Image type: same as screen in the Save Image dialog. Another way to save stereo images is by setting the Image type to stereo pair (cross-eye) or wall-eye stereo pair; in that case, 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, printing, and/or photocopying. The HEX color specifications at this site are Tk codes, which can be used as color names in many Chimera commands and in 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