These variables are set in top.js

in getMolToLoad()

validPDBId
// Contains a valid PDB Id if pdbToLoad was a valid PDB Id,
// or if the first four characters of pdbId are a valid PDB Id. Else blank.

var pdbURL; // URL Jmol uses to fetch the molecule.

pdbToLoad is the item between "mol=" and "&" if any.
It can be a PDB code or a URL.

pdbFilename is the PDB code or a filename at the end of a URL
(with everything up to the last slash removed).

usePDBId is a boolean saying whether or not to use validPDBId.

