rosetta3.4 fragment file problem

Member Site Forums Rosetta 3 Rosetta 3 – Applications rosetta3.4 fragment file problem

  • This topic has 4 replies, 3 voices, and was last updated 12 years ago by Anonymous.
Viewing 2 reply threads
  • Author
    Posts
    • #1280
      Anonymous

        In Rosetta 3.4, the fragment picker puts out a new format. AbinitioRelax does not recognize it. I get this error:

        ERROR: no fragment to compute secondary structure
        ERROR:: Exit from: src/core/fragment/SecondaryStructure.cc line: 68

        If I run exactly the same command but with the old style fragment files, it works fine. Is there something I’m missing?

      • #7124
        Anonymous

          I’m not aware of anything changing in fragment picking or AbinitioRelax for 3.4. I’ll ask around.

        • #7125
          Anonymous

            I realize now that the make_fragments.pl script option -old_name_format does more than keep the filename format the same. It actually changes the format of the fragment files. I’ve turned that option on by default in make_fragments.pl. I’m guessing fragment_picker is the same, but the make_fragments.pl script is different.

          • #7128
            Anonymous

              David Kim has made changes to make_fragments.pl that would have been released with 3.4, but he tells me none of the changes are to the format and that he wonders if it’s a platform issue.

            • #7136
              Anonymous

                Hi

                Yes, in general fragment_picker is the same, although from time to time someone adds extra columns on the right side of the file. I presume make_fragments.pl removes them when asked to do so. I don’t think the fact that now the file format is different causes any trouble; it has been extensively tested in ab-initio.

            Viewing 2 reply threads
            • You must be logged in to reply to this topic.