Flexible docking using rosetta density-fitting for DNA

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    • June 15, 2012 at 6:43 am #1309
      Anonymous

        Hi,
        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!

      • June 24, 2012 at 9:08 pm #7298
        Anonymous

          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?

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