Citat Modeller Caretaker modeller-care@salilab.org:
> 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 > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >