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I'm not sure if there is an effective answer to my problem, but here goes:

I am working on Ramachandran plots for short peptides (3 amino acids long). For every snapshot of the protein (this would be my data point) there are two angles being recorded, the phi and psi angles. Looks like this:

-144.369 -177.292

-64.5267 148.338

-114.061 141.662

-82.48 152.633

-64.7174 157.237

-85.9076 133.427

-103.411 145.982

-75.3895 150.165

Then I create several bins for the ranges that I'm interested in, so say I count how many of these data points have -160<phi<-120 and 140<psi<200. Once I have that count, I divide it by the total number of data points and find what percentage of the time the angles are in those ranges.

Now I need to calculate the standard error of mean for these percentages. I understand how to calculate the standard error of mean for the data itself, as in for the distribution of the data. But I am only counting how many data points fall into a given region and I am not sure as to how I can get an SEM for that.

Any help would be appreciated. And please ask if any clarification is necessary, even if you won't be able to help out, maybe it'll clarify things for the next person.

Thanks.