Membrane protein protocol on PyRosetta

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    • July 28, 2018 at 9:41 pm #2972
      Anonymous

        Hello Rosetta community

        I need to score a membrane protein using PyRosetta and am having trouble with the implementation.  The 2014 post in the forum has not been very helpful in terms of syntax, and there is little to no documentation. I see a tutorial is in the works on the website, but if anyone has advice right now that would be greatly appreciated. A working (minimal) example would probably be most helpful, something I can work off of. 

        Thank you

        Joel

      • July 31, 2018 at 7:59 pm #14348
        Anonymous

          Does it need to be in PyRosetta? I don’t use PyRosetta very often and I would suggest using the command line implementation. Detailed documentation is given in the Supplement of this paper. Before you score, just make sure the membrane protein is properly oriented in the membrane frame. Documentation for this is also given in the same Supplement. 

          https://doi.org/10.1093/bioinformatics/btw716

        • August 1, 2018 at 2:15 pm #14351
          Anonymous

            Hi jkleman

            I have windows and was having a lot of trouble downloading the orignal version of Rosetta. I stumbled onto PyRosetta on a virtual Bash shell as a compromise, and actually am really comfortable using it except there is a lack of documentation. Do you think the best way to proceed is to ditch PyRosetta and proceed with the original Rosetta software?

            -Joel

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