1atom.pdb is loaded (to enable echos) in view1SptPrefix (scripts.js).

The primary load command is in scripts.js, in makeJmolScript():

// LOAD
NEW METHOD to accommodate MODEL 0 in AlphaFold predictions:
finalSpt += "load MODELS ({0}) " + top.pdbURL + ";\n" +
This is the FIRST model regardless of its "MODEL #", could be 1 or 0.

OLD METHOD (thru 3.51)
finalSpt += "load " + top.pdbURL + model1 + ";" +
WHERE model1 IS ALWAYS " 1 " FOR JSMOL.