A single atom isolated somehow will, if you exite it via sunlight or electricity or heat radiation or whatever, send out photons of it's own, yes. It is not in any way dependant on surrounding photons to do so.
What I ment with magnify is that if we have a machine that picks up a single photon, and sends out 10 photons of the exact same type, our brain can see that as a coloured dot.
When we say atoms have a colour, we mean that the electrons of that atom sends out light with a certain frequency that is interpreted in the brain as colour. The other parts of the atom, like neutrons, does not send out light and are as such invisible. We still consider the light coming from the electrons as coming from the atom as a whole.
Wavelenght and frequency are directly related by a simple formula, in the case of light it's Frequency = Speed of light divided by Wavelenght. So each frequency have one specific wavelenght, since the speed of light is constant.
The wavelenght of an EM-wave is not related to how large the wave is, or how much space it takes up. It is only related to the shifting of the electrical (E) and magnetical (M) fields. A ray is completely straight.
The frequency also depends only on the EM properties of the ray, and describes how many 'peaks' (in field strenght) that passes a certain point per second.
None of these has anything at all to do with size or largeness; all light-waves are exactly the same size. It's just the behaviour of the energy it carries that changes.