Chimera Commands Index

set  keyword

( ~set | unset )  keyword

set  keyword  value

The following keywords indicate on/off toggles, where set keyword enables the option and ~set keyword or unset keyword disables it:

The following are used for value assignments with set keyword value: Keywords can be truncated to unique strings, and their case does not matter. Where multiple keywords start with the same word, an ambiguous truncation will be interpreted as the simplest keyword (for example, sil will be interpreted as silhouette).

See also: preset, linewidth, lighting, setattr, Effects, tips on preparing images, movie-related commands

set autoColor
Whether to give each newly opened model a different color; same as use new color... in the New Molecules preferences. For example, if the background is solid black or white:
 #0   #1   #2   #3   #4   #5   #6   #7   #8   #9 

See also: modelcolor
set bgColor  color
Sets the background color; color can be none or any color name that specifies a single color. Any transparency in the color will be ignored. Equivalent to background solid.
set bgTransparency
Whether to include opacity values (alpha) in PNG and TIFF image files saved from Chimera, to facilitate combining the images 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 in the Save Image dialog or with the startup option --bgopacity.
set depthCue
Whether to use depth-cueing, front-to-back shading of the scene.
set dcColor  color
Sets the depth-cueing color; color can be none or any color name that specifies a single color. Any transparency in the color will be ignored.
set dcStart  start
set dcEnd  end
Set the position of the depth-cueing ramp. Depth-cueing shading increases linearly from start to end, each expressed as a position relative to the front (0.0) and back (1.0) global clipping planes.
set echo
Whether to echo the line number and contents of each line in subsequently opened Chimera command files to the Reply Log and status line as that line is executed. Blank lines and comments (lines starting with #) are included.
set eyeSeparation  distance
Specify effective eye separation in millimeters for stereo.
See also: Camera
set fieldOfView  angle
Set horizontal field of view in degrees (allowed range 0°< angle <180°).
See also: Camera
set flatTransparency
Whether to make apparent transparency independent of the viewing angle. Otherwise, transparent triangles (forming objects as well as surfaces) will appear more opaque when viewed edged-on than when viewed face-on.
set fullscreen
Whether to use fullscreen mode, in which the graphics window fills the entire screen (available in Windows, Linux, and Mac-X11 versions of Chimera).
set independent
Whether to rotate models about their individual centers or a single collective center; set independent changes the center of rotation method to independent while ~set independent changes the center of rotation method to front center.
See the video mini-example. See also: cofr, focus, tile, Rotation
set maxFrameRate  N
Set the maximum frame rate in Chimera to N frames per second (default 60). Although N is the target value, the actual rate may be lower depending on the rendering speed of the computer and the complexity of the scene. The actual frame rate can be reported in the status line using the accelerator rt (command ac rt).
See also: frame rate and movie speed
set projection  mode
Which mode of projection to use: perspective, which makes farther-away objects smaller, or orthographic, which does not.
See also: Camera
set screenDistance  distance
Specify effective distance to screen in millimeters for stereo.
See also: Camera
set screenWidth  width
Specify effective screen width in millimeters for stereo.
See also: Camera
set shadows
Whether to show interactive shadows.
set showCofR
Whether to show “+” crosshairs (a plus sign) at the center of rotation. The plus sign will adjust to white or black for contrast against the background color, and will disappear when models are set to rotate independently (when the center of rotation method is independent).
set silhouette
Whether to show silhouettes, outlines that emphasize borders and discontinuities. This setting is global (applies to all models), but when it is on, silhouettes can be toggled for individual models with the command setattr, the Selection Inspector, or the molecule model attributes panel.
set silhouetteColor  color
Sets the color of silhouettes; color can be none (equivalent to black) or any color name that specifies a single color.
set silhouetteWidth  linewidth
Sets the linewidth of silhouettes.
set singleLayer
Whether to render only the topmost layer of all transparent items. Showing only the topmost layer rather than all transparent layers simplifies the display and is recommended for de-emphasizing transparent parts.
set subdivision  value
Sets subdivision level, where a higher value increases the apparent smoothness of stick, ball-and-stick, sphere, and ribbon representations by increasing how many planar facets are used to approximate them.
set subdivisionPixels  pixels-per-length
By default, the fineness of faceting of stick, ball-and-stick, sphere, and ribbon representations is adjusted dynamically based on:
  1. the subdivision parameter
  2. the pixel width of the graphics window divided by the width of the view at the center of rotation
Setting subdivisionPixels substitutes the specified static pixels-per-length for the second value above and suspends dynamic adjustment. This can enhance responsiveness to manual zooming (by precluding further subdivision calculations) and can speed up rendering by avoiding overly fine subdivisions that may occur with large windows and/or highly zoomed-in views. Setting pixels-per-length to zero or a negative value restores the dynamic subdivision behavior, as does ~set subdivisionPixels.