In the example provided, each colour codes for an individual polypeptide chain of the pentamer.

Definitely! 

That depends what is the color based on. You can make the colors based on polarity, mobility, but also on domain/chain

Thank you very much dear Tomas Hluska . previously my thought was its simply a color to distinguish the chains on the basis of different peptides.  can you please explain more ?  am attaching an acetyl choline binding protein , if possible please go through it once (what will be different color means)

In the example provided, each colour codes for an individual polypeptide chain of the pentamer.

Thank you Francisco J Barrantes

Sir, the above pic is taken from your paper "Unbinding of nicotine from the acetylcholine binding protein: steered molecular dynamics simulations"

Liu X1, Xu Y, Wang X, Barrantes FJ, Jiang H - It was my discussion in our last group meeting .

Yes, these are only different polypeptide chains to stress out their pentameric status and show how they bind to each other.