Filling color in layered objects (a few circiles on top of each other)

Hello all,
I am new to Illustrator. I want to thank you any advices from you all first.
Currently I am working on my first Logo design project. There are a number of circles on top of each other. The goal is to fill each circle with different colour.
I read some other posts, they mentioned about the different objects are in different layers, so that it is difficult to fill colour individually. Any suggestions?
I tried to make the image to Live Paint, but the option is in gray, so that I cannot change to Live Paint. And if I try to fill the colour, there are nothing happen.
The file (in .AI format) can be download from this link.
http://www.sendspace.com/file/olyyol
And one last question, after I completed the Logo, is that possible to just extract the Logo itself rather than save the whole paper? What type of format I should save with if I want to make it eventually jpg file.
Thank you very much for your help again.
Pete

You seem to be complicating this a little more than it need be.
here's video of what I did always keep it simple.
http://mysite.verizon.net/wzphoto/Paint.mov
As for what you did was possibly open another file or took an extra step.
But to do what you want is a very simple matter you should be able to figure this out yourself but i am going to try to show how you are making it comlicated rathe than easy.
First you fill one part with the color you want then
you fill the other part with the same color

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I figured I'd turn here for illustrator help since I'm a scientist and not terribly familiar with all the in's and out's of this program. I'm using Illustrator CS2.
I have a diagram of a 2D RNA structure. I want to give each nucleotide a numeric label and then write a program to change the color of a given nucleotide based on its number. That is to say, suppose I have a sequence ATTG. I want to label A-1, T-2, T-3, G-4. I then want to change the color of ATTG to other things from black by having a list. Make A blue, T green, T blue, G red. So I guess really my two questions are: How do I go about labeling the individual bases/objects and after doing so, is there a way to tell Illustrator to change an objects color based on a list structure. Thank you all for any help in advance.

function(){return A.apply(null,[this].concat($A(arguments)))}
They are individual objects. Text it appears. Each one is a text object.
Good. Then I'm going to assume, after opening the PDF in Illustrator, we now have an Illustrator document in which each text character is an individual text object.
function(){return A.apply(null,[this].concat($A(arguments)))}
Actually, I want to be able to color each object, independently, based on experimental data that will change each time....Sometimes A-1 will be green, sometimes red, sometimes black....For each of 1800 objects...[Emphasis mine.]
(I just love it when people ask "How can I do this?" and then casually inject schema-wrecking additional requirements later.)
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To my mind, we have also ruled out any practical application of a Variables-based solution, because Illustrator's Variable types are Visibility, Link, Text, and Graph Data. The attribute that is required to be variable is none of those four; it is color.
Therefore, at least at this point, a scripting solution seems to be the most promising approach.
Next question: How many colors, maximum, will be involved? Assuming there are, say, 2540 textFrame objects containing an A, surely you don't intend a potential of 2540 different colors for the As?
Knowing nothing about the actual information being represented by the diagram, and having so far received only piecemeal requirements, I have to make several other assumptions. Please correct me if any of these are wrong:
The diagram is fixed. For a given diagram, the count, location, and text content of the text objects will not change. You're not going to be changing a A to a B, for example. You're not going to add a spur to the diagram with additonal text objects. You're not going to be moving any of the text objects.
The ONLY attribute of the text objects you require to edit by applying different datasets is their color.
There will be a separate data table corresponding to each such fixed diagram. Each row in the data table will correspond to one and only one text object in the diagram.
function(){return A.apply(null,[this].concat($A(arguments)))}
I assume I'm going to have to go in and label/select/name each object, but if I can automate the coloring (based on data that will be in either a text or a excel file) I should only have to do it once on my reference file. Then each time I want to color it, I'll open my ref file, script out the coloring, then save it as EXP X.
You're asking how to work Illustrator here. And you've admitted being a complete beginner with Illustrator. So please don't run ahead by making assumptions about the necessary workflow. That just confuses the discussion. We are trying to think this through systematically, as I squeeze out of you the actual situation and the actual requirements. This is not a problem of data-exchange mechanism. It's an object-to-data correlation problem.
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To pursue this with Illustrator, the first task is going to be deciding upon a means by which to assign some Illustrator-understood object-level attribute that can serve as a unique identifier for each text object.
Based on what we know so far, the only obvious Illustrator-understood differentiation among the whole set of text objects is their text content: Each text object contains one of an assumed four different text characters. That gives us four subsets.
So, for now, think in the context of one of those four subsets: The ones containing the A character. In order to associate each A with a particular row in a data table, you're going to have to have some means by which to address each individual A.
Simply assigning a serial number to them, like "A1" thru "A2540", makes them targetable, and would be fairly trivial from a scripting standpoint. But a dumb serial number in no way relates to a particular row in the data that will, in turn, be used to assign their color. So before proceeding with that, it would be wise to consider whether there is any other criteria that might be leveraged to minimize the work of associating a particular text object with a particular data row. Otherwise, a two-step process will be required:
1. Assign meaningless unique identifiers to the text objects.
2. Associate the unique identifiers to the data rows. This will be a tedious manual process for each diagram, unless we can discover or devise some algorithm to reliably make those associations. Failing that, it may be possible to at least semi-automate the process by some intermediate step(s). Failing that, it may be possible to at least facilitate the process by some visual interface means. (More information will be requried in order to do that.)
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Within that subset of As, the only presently-existing Illustrator attributes to "latch onto" is position (X, Y) and stacking order (Z). Of those, (unless we are extraordinary lucky in terms of the creation order of the text frames correlating to the order of the data rows), XY position is probably the only viable attribute with which to individually lable the textFrame objects.
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