About secondary structure view in cartoon

[realbigws]

Just a minor question. If the protein model does not contain HELIX/SHEET assignment, then how to display the secondary structure in cartoon mode?

[biasmv]

You can use mol.assignHelixSheet(structure); to assign secondary structure based on a very simple algorithm. The algorithm is not as accurate as others, but it's a start. If you want to have very reliable secondary structure information, I suggest to run DSSP or a similar program on the server and store the secondary structure assignment in the PDB file.