I have followed Rosetta Density-fitting Tutorial to try to fit a B-form DNA into a segmented cryo EM map. The result after idealize and relax using default settings gave rise to a highly distorted DNA structure, very likely due to pushing all atoms into the density. The DNA within the EM map is supposed to be only slightly bent. I wonder if there is any special functions I can use to only do a rigid body fitting of the DNA based on information like helical axis extracted from the EM density. Thanks a lot!
I don't think there's an easy way to do what you want. I'm not sure Rosetta is parameterized for non-B-form DNA. Try constraints that make the DNA fold in the fashion you want?