The default colour scheme is as follows:
0= BLACK !Colour 0 - Background colour 1= WHITE !Colour 1 - Originally, WHITE 2= RED !Colour 2 - Originally, RED Used to highlight menu items. 3= GREEN !Colour 3 - Originally, GREEN 4= BLUE !Colour 4 - Originally, BLUE 5= CYAN !Colour 5 - Originally, CYAN 6= MAGENTA !Colour 6 - Originally, MAGENTA 7= YELLOW !Colour 7 - Originally, YELLOW 8= ORANGE !Colour 8 - Originally, ORANGE 9= 128 255 0 !Colour 9 - Originally, GREENYELLOW 10= 0 255 128 !Colour 10 - Originally, GREENCYAN 11= 0 128 255 !Colour 11 - Originally, BLUECYAN 12= 128 0 255 !Colour 12 - Originally, BLUEMAGENTA 13= 255 0 128 !Colour 13 - Originally, REDMAGENTA 14= 85 85 85 !Colour 14 - Originally, DARKGREY 15= 170 170 170 !Colour 15 - Originally, LIGHTGREY
These settings may be changed by substituting the appropriate keyword or red/green/blue colour values.
Users of full color, 24 bit displays, may make better use of the colours available, and so provide a more convincing 3D feel to the molecular visualiser, by using two extra features - depth cueing and antialiasing. These features are not available on older, 8 bit colour displays.
Both these features have pros and cons :
As a result, both these features may be configured to be either on, off, or at an optimum value for the display being used, by editing the ~/.Xdefaults file to include lines like the following:
pluto*depth:15 pluto*antialias: yes
The antialias setting determines whether antialiasing will be performed when a molecule is drawn, and may be either yes or no.
The depth setting effectively determines how much a display may be darkened by depth cueing. Values from 0 (no depth cueing) to 15 (lots of darkening) may be used.
By default, antialiasing is turned off, and depth cueing is set to 8.
Changes to the ~/.Xdefaults file only take effect when you next log in, or type the following command:
xrdb -merge ~/.Xdefaults
Both these features are experimental in the sense that it may not be worth having them turned on by default, so any feedback as to their usefulness or otherwise would be greatly appreciated.