Re: [modeller_usage] Objective Function vs. Molecular PDF

[Modeller Caretaker <>]

Leyla Celik wrote:
> In the end of the log-file from a MODELLER (8v1) run there is a summation of the
> quality of the model:

I recommend you use 8v2 rather than 8v1, as this corrects some bugs.

> > > Summary of successfully produced models:
>
> Filename                          molpdf
> ----------------------------------------
> A.B99990001.pdb        2355.08740
> N.B99990002.pdb        2376.38696
> ...
> ...
>
> My question now is if these values really are the molecular pdfs or if it is the
> objective function?

The two terms are interchangeable in this context.

> Another question: What is the default level of refinement actually? I have not
> been able to deduce this from the manual.

automodel is all Python code, so you can find out by looking at the code 
(in modlib/modeller/automodel/automodel.py) or simply by printing out 
the current value:

from modeller.automodel import *
env = environ()
a = automodel(env,
              alnfile  = 'alignment.ali',
              knowns   = '5fd1',
              sequence = '1fdx')
print a.md_level

This will print something like:
<function very_fast at 0x400794c4>

i.e. the default level of refinement is very_fast.

By looking up the very_fast function in 
modlib/modeller/automodel/refine.py you can see the exact annealing 
schedule used.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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