Re: [modeller_usage] automodel.max_molpdf recommended values and usage format

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 11/01/2011 10:28 AM, Andrew Voronkov wrote:
> 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.

	Ben Webb, Modeller Caretaker
--
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