I believe that one reason that one cannot compare molpdf scores
between models of different proteins is that it depends on the number
of atoms in the protein- more atoms means a higher molpdf, even if it
is a "good" model. Does this mean that if one is trying to do an all
hydrogen model that the molpdfs will be much higher than that for the
same protein modeled without hydrogens?
The reason that I ask is that I am modeling a pentamer with an all
hydrogen model, and each time the modeling stops after a few steps
with the moldpdf stuck slightly higher than 100,000 (which is the
default max_molpdf value) and then moves on to the next model, where
this happens again (and again...). I assume that this is because of
all of the additional hydrogens, and that if I just increase
max_molpdf to 200,000 things should be fine.