Flexible-backbone Rosetta design (partial flexibility)

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    • May 11, 2009 at 6:27 pm #465
      Anonymous

        Hi All,

        I have a question regarding flexible-backbone rosettaDesign. I have a protein complex with two chains, and I want to allow the backbone of only ONE chain (the smaller partner) to be flexible. However, although I have “resfile” specified in my run, the backbone of entire complex was moving freely and so the complex got unfolded. Here are the flags included in my run:
        -design -mvbb -read_all_chains -fa_input -repack -ex1aro -ex2aro_only -resfile

        Is it not possible to allow PART of the complex backbone to be flexible, or am I doing something wrong?

        Any input/information will be greatly appreciated

        Shirley

      • June 9, 2009 at 10:00 pm #4094
        Anonymous

          > Hi All,
          >
          > I have a question regarding flexible-backbone rosettaDesign. I have a protein complex with two chains, and I want to allow the backbone of only ONE chain (the smaller partner) to be flexible. However, although I have “resfile” specified in my run, the backbone of entire complex was moving freely and so the complex got unfolded. Here are the flags included in my run:
          > -design -mvbb -read_all_chains -fa_input -repack -ex1aro -ex2aro_only -resfile
          >
          > Is it not possible to allow PART of the complex backbone to be flexible, or am I doing something wrong?
          >
          > Any input/information will be greatly appreciated
          >
          > Shirley

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