Make_fragments.pl database

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  • This topic has 5 replies, 4 voices, and was last updated 3 years ago by Anonymous.
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    • #388
      Anonymous

        Anyone knows the right database to download from the ncbi site?
        The link in the rosetta tutorial is broken. I know that’s the nr one, but fasta formated or env.nr..
        any input on this?

        thank you

        tiago

      • #4237
        Anonymous

          > Anyone knows the right database to download from the ncbi site?
          > The link in the rosetta tutorial is broken. I know that’s the nr one, but fasta formated or env.nr..
          > any input on this?
          >
          > thank you
          >
          > tiago

          You can use UniRef90 from http://www.uniprot.org/. Fasta formated and you a have to run formatdb for setting up the psiblast database files. Just rename the UniRef90 fasta to nr and run

          ‘/my/blast/installation/formatdb -o T -i nr’

          David K

        • #4241
          Anonymous

            ok

            thanks ive had done and it worked, something to do with the index file, now it says it doesnt find the blosum65.iqj matrix, but its in the right directory. i just copied nnmake_database to my directory. does the script make_fragments.pl need more data from the fragments directory in rosetta.

            • #16012
              Anonymous

                Hi Tiago

                Where did you download nnmake_database?

                In the tutorial page it says provided with the release but I dont see anywhere?

                I have difficulty to modify the make_fragment.pl script as I dont find following database and ss prediction software sam?



                # nnmake
                my $VALL = "$scratch/$fragsDir/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database')
                my $VALL2 = "$scratch/$fragsDir/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database')
                my $VALL_NAME = "vall.dat.2006-05-05"; # filename of vall (vall.dat.<id> and vall_cst_coord.dat.<id> must exist)
                my $NNMAKE = $pathToDemo."scripts/frags/make.sh"; # nnmake binary (cvs respository 'nnmake')
                my $TRIMLOOPS = "$scratch/$fragsDir/nnmake/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake')

                # chemshift
                my $CHEMSHIFT = "$scratch/$fragsDir/chemshift/pCHEMSHIFT.gnu"; # chemshift binary (cvs repository 'chemshift')
                my $TALOS_DB = "$scratch/$fragsDir/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database')

                # jufo (secondary structure prediction software)
                my $JUFO = "$scratch/src/jufo/molecule.exe"; # jufo executable

                # sam (secondary structure prediction software)
                my $SAM_target99 = "$scratch/src/sam3.5.i686-linux/bin/target99"; # sam target99 executable
                my $SAM_uniqueseq = "$scratch/src/sam3.5.i686-linux/bin/uniqueseq"; # sam uniqueseq executable
                my $SAM_predict_2nd_dir = "$scratch/src/sam.predict-2nd/"; # sam predict-2nd directory
                my $SAM_predict_2nd = "$scratch/src/sam.predict-2nd/predict-2nd"; # sam predict-2nd executable

                Can anyone help me running make_fragment.pl?

                I also dont know what is the directory name: $fragsDir = “rosetta/rosetta_fragments_latest”;

                as I dont know anything about perl script does this means we create a directory and give path like this?

                 

                kind regards

                Mustafa

            • #16011
              Anonymous

                 

                Hi

                I am trying to use following link to generate fragments

                https://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/file_fragments.html

                but I cant find the nnmake_database given in the link. Can anyone share the correct link? and also help in running the make_fragment.pl as it fails to run due to failure of nr database download. However, if I select uniref96 it downloads correctly.

                kind regards

                Mustafa

              • #16026
                Anonymous

                  I am not familar with the Perl script described or fragments stuff in general, but I thought I’d mention that one can do this easily with PyRosetta too.


                  pose = pyrosetta.pose_from_file('****.pdb')
                  confragset = pyrosetta.rosetta.core.fragment.ConstantLengthFragSet(3)
                  pyrosetta.rosetta.core.fragment.steal_constant_length_frag_set_from_pose(pose, confragset)
                  print(f'{filename}: {confragset.nr_frames()} frames')
                  fragio = pyrosetta.rosetta.core.fragment.FragmentIO()
                  fragio.write_data('***.frags', confragset)

                  The pose can have ligands (not sure about DNA), but true to `ignore_unrecognized_res` and false to `load_PDB_components` in the init would seem wise.

                  The output is something like the following, which I belive the same as normal fragment files.


                  FRAME 1 3
                  1 0 no_pdb BBTorsion S L 0.000 125.451 179.413
                  2 0 no_pdb BBTorsion S E -158.982 169.226 179.818
                  3 0 no_pdb BBTorsion F E -85.818 153.494 174.140

                  This works fine within PyRosetta. Although, one can use them without wasting time writing to disk, but often its via a vector of it, eg.


                  fragsets = pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t(1)
                  fragsets[1] = confragset

                  ## Example: Threading
                  align = pyrosetta.rosetta.core.sequence.read_aln(format='grishin', filename='***.grishin')
                  threader = pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover(align=align[1], template_pose=template_pose)
                  threader.build_loops(True)
                  threader.frag_libs(fragsets)
                  threader.apply(threaded_pose)

                   

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