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 it in your pdb file before loading it in PyMOL, your cartoonish
rendering should be great :)

Cheers

Virgile ADAM



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