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.

• Adjust field of view - when the image size is specified in units of length, whether to use the specified image width instead of the graphics window width to compute the image field of view (details...). 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 camera mode of the graphics window is mono
  
  
• 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. 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 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, not necessarily to raytracing. While raytracing generates shadows and can give a more dramatic appearance, clearer and more illustrative high-quality images can be obtained in many cases 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 can also be changed with the set command (for example, set bg_color white), with Color Actions, or in the Background preferences. 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. Depth cueing can be adjusted with the Effects tool or the set command, or by moving the global clipping planes. The depth-cueing color can be changed in the Effects tool or with Color Actions.

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:

• 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). The level can be controlled with the Supersample setting in the Save Image dialog or the copy command's supersample keyword. For movies, supersampling is specified in the Frame Options section of Movie Recorder, or with the supersample option of the command movie record.

Transparency. Surfaces and other items can be transparent.

• Surfaces can be made transparent without otherwise changing their colors using the Actions... Surface menu (for surface models in general) or the command surftransparency (molecular surfaces only).
  • Whether to render only the topmost layer or all layers of a transparent surface can be set using the Actions... Surface menu. Showing only the topmost layer simplifies the display and de-emphasizes surface ripples and folds.
  • 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, ribbons can be assigned transparent colors. This more general approach also works 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.

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. Text, symbols, and arrows can be added to the display with the 2D Labels tool (or command 2dlabels). 2D labels and arrows of multiple colors and sizes can be placed anywhere in the plane of the graphics window (without "depth"), appear in front of any displayed objects, and do not move when models are moved. In contrast, the standard Chimera labels (shown with the Actions... Label menu or the commands label and rlabel) are tied to atoms in 3D and will move along with them. The spatial offsets of 3D labels can be controlled with label/rlabel and adjusted interactively with the mouse, but their size can only be adjusted collectively in the Background preferences. 3D arrows can be created in BILD format, and other 3D objects can be created in that format or with the command shape.

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.

Color schemes. Several factors should be considered in color scheme design, including what the colors are meant to indicate, how the data are presented, 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