how on your opinion modeller objective function correlates with
quality of the models. For example I have objective function value
1730 for one modelk and -750 which as I understand reflects free
energy. Does it mean that I shouldn t consider the first one at
all?
The Modeller objective function is simply a measure of how many
restraints were violated in building your model. While the score could
be thought of roughly as an "energy" (not free energy) this is certainly
not a rigorous measure of model quality. Use an assessment function such
as normalized DOPE for this purpose.
Let's say I want to make cutoff -100 for the objective function. In
which format it should be done?
automodel.max_molpdf -100
Build your models, then assess them and pick the best ones. max_molpdf
is designed as a filter to throw away the very worst models - it doesn't
act on the final PDF, but the score of intermediate (partially
optimized) models - the reasoning being to not waste time on trying to
optimize a model that is very bad. Thus max_molpdf is not really what
you want here.