17 Nov
2008
17 Nov
'08
6:31 p.m.
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.
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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 |