fragment_picker with fasta only

Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › fragment_picker with fasta only

Viewing 3 reply threads
  • Author
    Posts
    • November 15, 2011 at 9:20 pm #1085
      Anonymous

        I would like to generate a fragment library based on a sequence. I tried running the fragment_picker demos in rosetta3.3/rosetta_demos/fragment_picker and it seems I need to include a pdb and also psipred (.ss2) file. The documentation seems to say that only vall .fasta .wghts are mandatory. I only have sequence — can I still run this protocol?
        http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_fragment_picker.html

        I think if I don’t have any third party secondary structure information or a pdb I somehow need to change the .wghts file. For instance the .wghts given in the demo reference predA (BestFragmentsProtocol/input_files/simple.wghts) or psipred, sam, jufo (QuotaProtocol/input_files/quota-protocol.wghts).

      • November 15, 2011 at 9:26 pm #6266
        Anonymous

          A) You can try changing the weights to zero in the weights files you mention. There should be a real-number-valued column to change to zero (or try deleting those rows). I don’t know which weight to leave on for sequence-only prediction; play around or maybe it’s in the documentation?

          B) You can create dummy secondary structure prediction (all loop, if you prefer) and run with that?

        • November 15, 2011 at 9:46 pm #6267
          Anonymous

            > it seems I need to include a pdb and also psipred (.ss2) file.
            You need to provide the query amino acid sequence. It may come in the form of FASTA file, PsiBlast checkpoint or a PDB file. psipred file is not required. Assuming that you have only the FASTA file, your weights file would look as follows:

            RamaScore 150 2.0 -
            SequenceSimilarity 200 2.0 -

            and your flag file:

            -in:file:fasta query.fasta
            -in:path:database ../database/
            -in:file:vall vall.dat.apr24.combo.aug09.gz
            -frags:n_frags 200
            -frags:n_candidates 200
            -frags:frag_sizes 9 3
            -frags:bounded_protocol

            Note, that without secondary structure prediction, you can’t use the quota protocol

          • November 19, 2011 at 12:03 am #6278
            Anonymous

              Thanks! I got it working… the only change that SequenceSimilarity is not recognized as a score type. Perhaps you meant SecondarySimilarity – but this doesn’t seem to work with just a fasta file. In the end I generated some fragments with this *wghts file:

              RamaScore 150 2.0 -

              Robetta (which isn’t as flexible as fragment_picker) generates the .jufo_ss, .psipred, and .psipred_ss2 files which can be used this fragment_picker protocol

          • Author
            Posts
          Viewing 3 reply threads
          • You must be logged in to reply to this topic.