Re: [modeller_usage] Objective Function vs. Molecular PDF

[Leyla Celik <>]

Citat 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.

Yes, but 8v2 was not released when we built our initial models and we would like
to be able to compare the works directly.

> 
> >>>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.

But as far as I understand the objective function is -ln(mol pdf)... I have two
models from the same alignment run in modeller at two different times, one with
a value of ~2000, the other at ~8000. If these represent the objective function
the first model would be the superior whereas it would be the opposite if it is
the molecular pdf. As I see it, there is quite a difference here!

Leyla


> 
> 	Ben Webb, Modeller Caretaker
> -- 
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
> 


-- 
Leyla Celik
Ph.d. student
Department of Chemistry
University of Aarhus
Langelandsgade 140
DK-8000 Aarhus C
Denmark
Tel: +45 8942 3869
e-mail: