Fragment files for membrane_abinitio application

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    • February 14, 2011 at 4:34 am #785
      Anonymous

        Hi

        I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
        make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta

        The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.

        Could anyone please help in this matter ?

      • February 14, 2011 at 2:54 pm #5015
        Anonymous

          I have moved your post to the 3.x forum and asked one of the membrane abinitio people to take a look at it.

        • February 14, 2011 at 5:37 pm #5018
          Anonymous

            Hi,

            The span file specifies only approximate positions of transmembrane regions – it does not specify how many residues you will get in a transmembrane helix. The number of residues in a transmembrane helix depends on the secondary structure prediction for that region (that is reflected in the fragments library). I would recommend to try to use only SAM secondary structure prediction file (*.rdb) to generate the fragments – see rosetta3.2 manual:
            http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/membrane_abinitio.html,
            where we have the following advice:
            “Generate structural fragments only using SAM secondary structure prediction file (*.rdb) – jufo and psipred predict transmembrane helical regions poorly.”
            If it does not help, then according to the secondary structure prediction methods used by rosetta, that helix is not predicted to contain ~30 residues.

          • February 16, 2011 at 1:10 am #5029
            Anonymous

              They may be fragment files – did you open one up in a text editor to see if it looks like a fragment file format? If they aren’t, I’ll ask varovoy again for help…

            • February 16, 2011 at 2:20 am #5035
              Anonymous

                You don’t need to generate .rdb file on the SAM server – just generate fragments using the following command:
                ~tex/src/nnmake/make_fragments.pl -id test_ -nopsipred -nojufo -verbose test.fasta

              • February 15, 2011 at 6:11 pm #5023
                Anonymous

                  Thanks a lot….

                • February 15, 2011 at 8:19 pm #5026
                  Anonymous

                    Hi

                    As recommended by you, I used SAM secondary structure prediction server and got results. It produced many *.rdb files. Can you tell me how to use these *.rdb files to generate fragment files (frag3 and frag9) ?

                  • February 16, 2011 at 1:26 am #5032
                    Anonymous

                      Hi

                      I checked in the text editor, they are not the fragment files. Could you please ask Vladimir for help . It would be greatly appreciated. Thanks.

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