I am displaying hydrogen bonds using:
distance hbond, protein, ligand, mode=2
which makes some nice dashed lines for hydrogen bonds but
doesn't always display all the hbonds one might expect.
For instance, in some cases there are is an N on the
ligand molecule and a backbone amide 3.2 A away but it
doesn't get drawn (and others, both longer and shorter,
do). By contrast, if I turn on roving_detail, this
connection does get drawn. I had thought that the
distance command with mode=2 might be purely based on
distance, but is it also estimating whether geometry is
suitable or is it perhaps having trouble due to ignorance
of the bond order of the ligand (i.e. N versus NH since
hydrogens are not explicitly present)?? I know I can draw
hbonds manually, but I'm hoping for an automated process
good for the long-term.