Thanks for the answer! That explains it. I was looking just at the amino acid sequence and missing a whole lot. I read the protein folding and X-ray crystallog

Thanks for the answer! That explains it. I was looking just at the amino acid sequence and missing a whole lot. I read the protein folding and X-ray crystallography articles on Wikipedia and they had most of the answers I was looking for. I also saw a request being made by this JavaScript 3D viewer to fetch the PDB (Protein Data Bank) file for the model, which is a text file with tens of thousands of lines describing the coordinates of atoms in space as well as their bonds and other structures. It even has some metadata about the way the data was collected. For the spike protein linked above: http://files.rcsb.org/view/6X6P.pdb http://files.rcsb.org/view/6X6P.pdb I find it fascinating that we're even able to scan the 3D structure of molecules with such precision.