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!
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Flexible docking using rosetta density-fitting for DNA