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? I've seen in other
examples something like the following for complete models:

# 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)?

Thanks again for all your help.

--
0 | Mauricio Carrillo Tripp, PhD
/ | Department of Molecular Biology, TPC6
0 | The Scripps Research Institute
\ | 10550 North Torrey Pines Road
0 | La Jolla, California 92037
/ |
0 |