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