[modeller_usage] Objective Function vs. Molecular PDF

[Leyla Celik <>]

Hello,

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

>> 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 reason I am asking is, that we have built homology models of the same
protein two times using the same sequence alignment and template pdb-files only
changing the refinement level - one is the default the other is md_level =
refine.slow_large.

In the second run the values in the log-file range around 9000. If the value
really represents the mol PDF this is good, but if it is the objective
function, the first models (default refinement) with the lower values are much
better...

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

I hope someone can help me with this:-)

Thanks in advance
Leyla


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