Colors can be specified in commands (color, etc.) with:
The command color list lists the available names along with color swatches in the Log. Color names can be truncated, with ambiguous truncations going to the shortest of the matching full names. For the color command, however, color names starting with “pale” should be expanded sufficiently and enclosed in quotation marks (or the space omitted) to distinguish them from the palette option. See also: initial colors, element colors, palettes, command usage conventions, limitations of transparency
The following color names (X11 colors from the CSS3 specification) are predefined in ChimeraX. Color names can be truncated, but they must be entered in lowercase only. The spaces in multiword names are optional, and “grey” may be substituted for “gray.” More names can be defined with the command color name. See also: Color Actions, the Actions... Color menu
The following all specify the same color:
redThe following specify the same shade of gray:
rgb(255, 0, 0)
rgb(1., 0., 0.)
rgb(100%, 0%, 0%)
rgba(100%, 0%, 0%, 1)
rgba(100%, 0%, 0%, 100%)
hsl(0, 1.0, 0.5)
hsl(0, 100%, 50%)
Objects can be made transparent by including transparency (alpha < 100%) in command-line color specifications. In addition, the transparency command or the color command transparency option can be used, as well as the system color-editing dialog (e.g., shown by using menu: Actions... Color... From Editor).
Unfortunately, ChimeraX does not correctly render transparency when there are multiple transparent models, with the exception of multichannel volume data rendered in the image display style.
As in Chimera, ChimeraX does not correctly render the transparency of multiple models because it draws one model at a time and only keeps track of the front-most as drawing occurs. When more than one model is transparent, ChimeraX shows only the frontmost transparent model at each pixel position. Any transparent models that are behind another transparent model will simply be invisible. An alternative to transparency for surfaces is to show them in the mesh style. Since rendering is correct for opaque models behind transparent ones, another possibility is to make only the outermost surface transparent, keeping inner objects opaque.