Re: [modeller_usage] max_molpdf and all hydrogen models
To: Mike White <>
Subject: Re: [modeller_usage] max_molpdf and all hydrogen models
From: Modeller Caretaker <>
Date: Tue, 24 Oct 2006 12:43:58 -0700
Cc: ModellerUsage List List <>
Mike White wrote:
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?
Yes.
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.
You can certainly try increasing max_molpdf; however, this could also be
an indication of a bad model, so you should check the results carefully.
The default is to build models without hydrogens, since including them
increases computational time roughly 4X and most crystal structures do
not include them anyway.