Here is a script that does what I think you are requesting. Each monomer in the aggregate is represented by a circle. I will use 3 figures to illustrate this:
Above: Possible circles to use for each monomer, ranging from diameter d=6 pixels to d=20 pixels.
Above: Aggregate array with d=10. Inset: original aggregate, 1 pixel per monomer.
Above: Aggregate array with d=20. Inset: original aggregate, 1 pixel per monomer.
I think the image with d=10 is just as good as the one with d=20, so I recommend it, since it takes up 4 times less memory than the image with d=20. You can change d in the script, run it, and decide.
