I can modify the colors of carbons in Coot under Edit, Bond Colours..., but that only gives me different hues. Is there a way to change the color to something less-saturated (or perhaps slightly transparent) so I can identify the "active" molecule I'm working on versus a template?

The menus seem no help, I'm wondering if there's some scripting magic that can do this.

  • $\begingroup$ @Rory, they're not buttons $\endgroup$
    – Nick T
    Feb 2, 2012 at 21:20

1 Answer 1


You could try other visual differences, like make what you're interested in ball-and-stick, and everything else wireframe, like in this example:

like on this example.

.... Because, from: http://www.ysbl.york.ac.uk/~lohkamp/coot/doc/coot-python.html

procedure: hilight_binding_site (imol, centre_residue_spec, hilight_colour, radius): hilight-colour is specified in degrees (round the colour wheel - starting at yellow (e.g. 230 is purple))

It looks from this like you only get to choose Hue (color_map_rotation) and not Saturation or Lightness, even with the script interface.

However, text can be full RGB

3.28.3 (set-font-colour red green blue)


red is an inexact number green is an inexact number blue is an inexact number


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.