Well, you're only modeling portions of proteins. Probably 20-40 amino acids at a time. It's too hard to do anything else, especially as some multimeric proteins can have thousands of amino acids.
Methionine is rare. It's unique to the first amino acid position in the chain. You'll only ever have one of those, regardless of how big the protein is. Cysteine is pretty rare too - it's usually found in the active site, which makes sense why you'd see it in the folded "pocket" of the peptide. Most of the amino acids found in a protein (ala, leu, gly) have R-group hydrocarbons, which explains all those grey and white atoms!
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