The Paint commands affect the colour properties of molecules or molecular objects. Each molecule has an associated atomic property called [mol]_atom_colour, and each molecular object has a property called .obj_col_[object name]. These are integer arrays of colour values. The difference between these two lists of colours is subtle, but it is important that the difference between them is understood. If you make a molecular object, for example using the command Zone or Ca , the current colour property of the molecule is copied to the object colour array. Therefore, you can make an object of a molecule coloured according to element type, with carbons white, oxygens red etc. Now, you can change the colours associated with each atom, to represent, for example the magnitude of their temperature factors, and make another object. Now there are two objects, representing the same molecule. However, the colours of the first object you created (the one with atom colouring) did not change when you changed the colour property of the molecule, because they are saved in the O database along the description of the object.
Some of the commands in the Paint menu change the colour property of the objects. These are Paint_object, Paint_obj_zone and Paint_obj_atom, and can be used to colour objects with the current active colour, set by Paint_colour. The molecular colours have to be set according to some atom or residue property. There is a selection of commands for doing this in different ways, namely Paint_property, Paint_ramp, Paint_case and Paint_zone.
O makes use of the RGB (Red-Green-Blue) colour scheme, where the relative intensities of the three major colour components are set, using numbers between 0.0 and 1.0. Thus, red is (1,0,0), blue is (0,0,1) and so on. In the program, these three numbers are converted to three 8 bit numbers between 0 and 255, and packed into a 32 bit integer word. These numbers (referred to as colour codes) are extremely strange when written out in decimal format, and are not understandable by normal human beings. Unless you're really into changing certain datablocks in the database, you should never have to deal with these strange colour codes. The normal way to specify colours in O is by typing the name of a colour. In the default startup.o and colour_default.o files, there are 71 colours to choose from and are the colours defined in X-windows. These are
O > pai_col ? Paint>Available colors: Paint> aquamarine black blue Paint> blue_violet brown cadet_blue Paint> coral cornflower_blue cyan Paint> dark_green dark_olive_green dark_orchid Paint> dark_slate_blue dark_slate_gray dark_slate_grey Paint> dark_turquoise dim_gray dim_grey Paint> firebrick forest_green gold Paint> goldenrod gray green Paint> green_yellow grey indian_red Paint> khaki light_blue light_gray Paint> light_grey light_steel_blue lime_green Paint> magenta maroon medium_aquamarine Paint> medium_blue medium_forest_green medium_goldenrod Paint> medium_orchid medium_sea_green medium_slate_blue Paint> medium_spring_green medium_turquoise medium_violet_red Paint> midnight_blue navy navy_blue Paint> orange orange_red orchid Paint> pale_green pink plum Paint> red salmon sea_green Paint> sienna sky_blue slate_blue Paint> spring_green steel_blue tan Paint> thistle turquoise violet Paint> violet_red wheat white Paint> yellow yellow_green
If this is not enough for you, the program will in most places accept 3 numbers for the RGB value when the colour prompt comes up. You can also define your own set of colour names. To get the list of colour names, type a question mark (?) as argument to the Paint_colour command. When specifying a colour name, you are allowed to abbreviate to a unique set of letters.
(If you insist on fooling around with the strange colour numbers, for modifying menu.o, for example, there is a macro @colcod to do the conversion for you).