The atomic percentage is the number of atoms of that element, at that weight percentage, divided by the total number of atoms in the sample multiplied by 100.
So the atomic weight percent is calculated from the element weight percentage by dividing each element weight percentage by its atomic weight, do this for all elements in the sample, you will have a list of atomic proportions. Sum these together to obtain a total atomic weight. Then for each element in the sample divide its atomic proportion by the total and * 100.
Here is an example - using pyrite. EDX will give you
Fe: el wt% 46.55
S: el wt% 53.45
divide each by their atomic weights Fe (55.85) S (32.06) and sum
Fe: 46.55 / 55.85 = 0.833
S: 53.45 / 32.06 = 1.667
divide each by the sum (2.5) and turn into atomic percentage