There's something I don't understand about protein shapes. There are tons of software solutions – on the web and offline – to visualize the shape of proteins from their sequence of amino acids. How do these work then, if we don't know how the atoms might be arranged in space?

For example, this[1] is the code for SARS-Cov-2's Spike(S) protein. From what I understand of this page it's pretty short, only ~1,757 proteins (corresponding to ~3,821 bases in RNA).

And here[2] is a visualization of it in 3D. You'll likely recognize the characteristic mushroom shape that's been portrayed in 3D models of SARS-CoV-2 in the media. How does this software work if there's no real way to tell how the protein is arranged?

[1] https://www.ncbi.nlm.nih.gov/nuccore/NC_045512 (search for spike glycoprotein on that page)

[2] https://3dmol.csb.pitt.edu/viewer.html?pdb=6X6P&style=stick&...