make_fragments

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    • September 21, 2009 at 7:42 pm #373
      JianyiYang
      Participant

        We are trying to install make_fragments.pl locally still. Does anyone know about the neuralnet file that results from predict_2nd site? It seems to call overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net, but the predict_2nd package seems to have this:
        t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-stride-seeded.net

        Thanks,
        Christy

      • September 25, 2009 at 5:15 pm #4200
        Anonymous

          > We are trying to install make_fragments.pl locally still. Does anyone know about the neuralnet file that results from predict_2nd site? It seems to call overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net, but the predict_2nd package seems to have this:
          > t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-stride-seeded.net
          >
          > Thanks,
          > Christy

        • September 25, 2009 at 5:17 pm #4201
          Anonymous

            I run make_fragments for CS-ROSETTA, and I’ve found, that, personally, I didn’t need to run predict 2nd (I couldn’t get it to compile properly, and I didn’t really have the time to figure it out. ) Make_fragments works without all the secondary structure files.

          • February 7, 2011 at 9:21 pm #4981
            Anonymous

              Bump.

              Christy, did you ever find this file? I sent you an email via the forums tool, but I’m not really sure it’s working.

              I seem to have basically followed Christy’s steps in getting the make_fragments.pl tool, and I’m currently stuck on the missing overrep-3617-IDaa13-7-10-11-10-11-7-7-ebghtl-seeded3-stride-trained.net file used by predict-2nd. Has anyone actually put together a working make_fragments script?

              Presumably Kevin Karplus has or knows how to generate this file, so I guess I’ll ask him next.

            • February 7, 2011 at 9:59 pm #4982
              Anonymous

                “Christy, did you ever find this file? I sent you an email via the forums tool, but I’m not really sure it’s working.”

                Probably not – this thread was imported from the “old forums” but the user data was not transferred, so there’s probably no recipient listed for that email.

                (No, I don’t know how to do the fragments, unfortunately…)

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