Modeling of side-chains onto membrane ab initio cluster?

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  • This topic has 3 replies, 3 voices, and was last updated 13 years ago by Anonymous.
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    • June 23, 2011 at 11:03 am #958
      Anonymous

        Hi all,

        I am running a big membrane ab initio calculation and clustering right now. So far everything ran well, and clustering gave me good results.

        Now I want to remodel the best cluster into a full structure with amino acid side chains and so on. So I’m searching for an application in Rosetta, that can generate a full structure out of the low-resolution centroid models? As far as I know the original ab initio application switches between centroid modeling and refinement, so it should be possible to complete this task.

        thanks a lot,
        akfried

      • June 23, 2011 at 1:42 pm #5805
        Anonymous

          I believe the relax executable is used for this purpose.

        • July 2, 2011 at 10:15 pm #5830
          Anonymous

            The manual indeed states that it can read centroid models. Thank you!

          • July 23, 2011 at 9:34 pm #5901
            Anonymous

              hi akfried, could you please go through with me the steps you used for your membrane ab initio calculation and clustering? i have a 97aa membrane protein that i want to perform membrane ab-initio on.

              your help is greatly appreciated.
              thanks.

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