Paul,
If I remember correctly, "color monomer" is an alternative to "color group", 
that is, it colors by 
residue, not by chain.

Andreas,
only blue and yellow? then it's sure hard.
The problem is, "color chain" relies on the chain ID, and you cannot assume 
that all pdb files 
will use chains A, B, C etc. Some of them use R, N, J and F for example. That's 
why we need 
the 26 colors.

Another choice is to select each chain and specify a color by script. You might 
have a generic 
coloring script or script file that says e.g.

select *:A; color whatever; select *:B; color whatever; select *:C; color 
whatever; [...]

Or maybe the user colorscheme is the way to go for this.




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