rmsd and Lrmsd in loop modeling

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    • January 24, 2012 at 5:52 pm #1143
      Anonymous

        Hi,

        I have a question about output file test_loop_output.fasc in
        an example of Cyclic Coordinate Descent loop closure – loop_modeling.py.
        Here we have rmsd and Lrmsd, what is the difference?
        In manual you can find that Lrmsd is the rmsd of all loops in the reference
        frame of the fixed protein structure.
        What does it means? What is rmsd?
        How to find rmsd for all loop backbone atoms?

        Thank you,

        Victor

      • January 25, 2012 at 5:23 pm #6576
        Anonymous

          Hi Victor,

          loop_moodeling.py is deprecated, please see test/T650_LoopsKIC.py and test/T660_LoopBuilding.py for reference.

          Sergey.

        • January 27, 2012 at 4:13 pm #6589
          Anonymous

            Thank you.

            Victor

          • January 30, 2012 at 4:07 pm #6596
            Anonymous

              Hi Sergei,
              Thank you again for information on 650_LoopsKIC.py and T660_LoopBuilding.py . Unfortunately I did not find any explanations for these files.
              If I want to generate N decoys, how to extract pdb files and rmsd (or Lrmsd) and scoring functions from them?
              What difference between 650_LoopsKIC.pyand T660_LoopBuilding.py files, and what is new comparison to loop_modeling.py
              I really appreciate for your help.
              Thank you, Victor

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