Hi Claudia,
those clash visualizations are drawn by the sculpting routine, so you
have to invoke sculpting in some way to get them.
This python function creates a copy of your selection, does one
sculpting cycle and shows bumps for it:
from pymol import cmd
def show_bumps(selection='(all)'
Please, I have modelled several mutants of a protein with FoldX and I would
like to display the clashes present in each case in PyMol.
I have seen that activating the "mutate" wizard I can display clashes with red
disks, but only for standard rotamers, which are not those tipically used by
Fold
