Decoy Clustering

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    • February 2, 2010 at 6:50 am #435
      Anonymous

        Has anyone found/written a decoy clustering script for PyRosetta? If no one has, I will post mine once it’s done.

        PyRosetta Team: Will we soon be able to upload our own scripts to the PyRosetta Database?

      • February 4, 2010 at 3:20 am #4327
        Anonymous

          We are still working on adding script upload functionality with the website. In the meantime if you email pyrosetta@graylab.jhu.edu with a zip file containing your script, input files, and instructions for how to use it, we will test it out and put it on our website (crediting the writer of the script, of course).

          There currently is no script for decoy clustering in PyRosetta.

        • February 4, 2010 at 2:41 pm #4330
          Anonymous

            > Has anyone found/written a decoy clustering script for PyRosetta? If no one has, I will post mine once it’s done.
            >
            > PyRosetta Team: Will we soon be able to upload our own scripts to the PyRosetta Database?

            There are scripts for decoy clustering in the regular Rosetta package, including scripts appropriate for handling docking output. The regular Rosetta package is available through the RosettaCommons (http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/rosetta.php) and you can simply look in the scripts/ directory.

            Perhaps we should package some of these support scripts with PyRosetta?

          • February 5, 2010 at 6:23 pm #4337
            Anonymous

              Jeff,

              That would be wonderful. Maybe V 1.2?

              Sid,

              That sounds great. As soon as I have some finished scripts that may be useful to others, I’ll send them in. Perhaps when you do implement the ability to upload, each person/lab can have their own kind of small database. We can upload, with a description/usage instructions. Each script can maybe have a comment section to further development, exchange, and collaboration b/t groups. By having each person’s scripts clustered like this, it will be easier to learn + help each members slight programming differences, and may further our own (and your) work.

              -Jared

              P.S.

              Any way to add basic formatting (like indentation) in the forum?

            • February 4, 2013 at 11:00 am #8363
              Anonymous

                I have top 500 structers after flepepdock ab-initio run which i want to cluster. I have start.pdb, start.ppk.pdb and 500 srructers. How to cluster the structures.

              • February 4, 2013 at 12:32 pm #8364
                Anonymous

                  solved…

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