Hi Kristl
The problem is that the secondary structure of your protein hasn't been
defined in the PDB file. This is why the cartoon looks ike a tube. What
you need to do is type util.ss into the command line and this will
calculate some sort of secondary structure for you although it's not
that acc
Have you set your sheet and helix part in your pdb? For my personal case,
things you experienced happened when this part wasn't built.
I guess that PyMOL cannot find the secondary structures as softwares like
Rasmol can.
Try to determine your secondary structures with DSSP for example and to
paste
