When I save the state or write the state to a script in Jmol 11.3.6, areas of cartoon that are neither helix or sheet balloon up into large tubes when the state is restored or the script is run.
This does not happen if I simply open a pdb file, put it into cartoon, save the state, and restore, but it does happen in a complex script I am working on (attached). I will send the script to Bob under separate cover.
Bob, when you open the script you'll see al the ugly tubes; to test it,
the tubes will go away - now save the state, and restore.
The tubes are back.
Molecules in Motion
Interactive Molecular Structures