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 http://salilab.org/modeller/9v5/manual/node44.html
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 functions.
> # 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