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[modeller_usage] refinement of protein-DNA complex


I use Modeller 9v5 for modeling protein-DNA complex. I include DNA
during modeling. I wanted to try with optimization of protein-DNA
interface using a.md_level = refine.slow_large and noticed that
although the protein part changes significantly comparing to the
template, the DNA part stays very similar to the template. Should I
use another method for turning on the optimization of DNA itself? Or
better I should not try with optimization of DNA using Modeller ;-) ?

Janek Kosinski