Subject: Re: [modeller_usage] Loop model refinement level
From: Modeller Caretaker <>
Date: Mon, 17 Nov 2008 21:30:53 -0800
Mauricio Carrillo Tripp wrote:
> In the example taken from http://salilab.org/modeller/manual/node32.html,
> the loop refinement level is set to "fast"
> a.loop.md_level = refine.fast # Loop model refinement level
> What other levels of refinement do I have access to?
See http://salilab.org/modeller/9v5/manual/node74.html and
The refinement level is simply a Python function which, given a
selection of atoms from your model, performs molecular dynamics. See the
refine module (file modlib/modeller/automodel/refine.py) for example
> # Very thorough VTFM optimization:
> a.library_schedule = autosched.slow
> a.max_var_iterations = 300
> # Very thorough MD optimization:
> a.md_level = refine.very_slow
> # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6
> a.repeat_optimization = 3
> a.max_molpdf = 1e8
> Would this also apply for loops? Would it make much difference in terms
> of final model/loop quality (DOPE score maybe)?
You can see all the adjustable parameters in the modeling class
reference at http://salilab.org/modeller/9v5/manual/node40.html. You can
see from that reference that some similar parameters can also be set for
loop refinement, but probably the only one that makes a great deal of
difference is a.loop.md_level. Generally speaking we find that building
a larger number of models is better than trying to build a small number
of "high quality" models.
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage