Displaying ribbon/cartoon in CA-only PDB files with PyMOL

PyMOL is a molecular visualisation program that takes PDB files and reads all those ATOM lines and shows their pictoric representation. Usually protein PDB files have more than just the carbon alpha backbone information. They have side chains and the atoms involved in the peptide bond, as well as some heteroatoms ( co-factors, metals, ions, … ). And all this information is read to give you back a nice picture of your protein. However, if you have a PDB file that only contain CA coordinates and you load it in pymol it will not look nice by default. Here’s how you get it to display a bit better your protein.

This is what I get from loading a CA-only PDB file on PyMOL 1.2:

The trick to make it display either ribbon/cartoon is to turn on an option that PyMOL disables by default:

set cartoon_trace_atoms, 1

set ribbon_trace_atoms, 1

I enabled both and then displayed either cartoon or ribbon. The results are shown below. It helps for a better visualisation. Also, remember that since you’re having only CA atoms, the cartoon representation will not be able to draw fancy secondary structure elements (B-sheets, A-helices).

set cartoon_trace_atoms, 1

set ribbon_trace_atoms, 1

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