[modeller_usage] max_molpdf and all hydrogen models

[Mike White <>]

Hello,

	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.

Is my underlying assumption correct?

Thanks