Thanks Joseph and Thomas for your replies. When I use the "as cartoon" commands, all my molecule disappear. My *pdb file could be the problem as it is a *cif crystal structure file (converted with mercury) from the cambridge crystal data.


2011/8/16 Thomas Holder <>
Hi Baptiste,

I have a small helical pseudopeptide with mixed alpha and beta amino-acids. How can I make a cartoon representation of this helix with Pymol? For the moment, I have selected the peptide backbone atoms and tried the "alter" command to force pymol to recognize the helix but it do not work.

are you sure? What happens if you try this:

alter all, ss='H'
as cartoon


Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen